FoundationOne Liquid CDx (F1 Liquid CDx)

{0} # SUMMARY OF SAFETY AND EFFECTIVENESS DATA (SSED) ## I. GENERAL INFORMATION Device Generic Name: Next generation sequencing oncology panel, somatic or germline variant detection systemDevice Trade Name: FoundationOne® Liquid CDx (F1 Liquid CDx)Device Procode: PQPApplicant's Name and Address: Foundation Medicine, Inc. 150 Second Street Cambridge, MA 02141 Date(s) of Panel Recommendation: None Premarket Approval Application (PMA) Number: P190032/S001 Date of FDA Notice of Approval: July 15, 2021 The FoundationOne® Liquid CDx was approved on August 26, 2020 as a companion diagnostic for *BRCA1* and *BRCA2* alterations in metastatic castration-resistant prostate cancer (mCRPC) patients who may benefit from treatment with RUBRACA® (rucaparib) and *EGFR* activating mutations (Exon 19 deletions and L858R substitution mutation) in patients with advanced and metastatic non-small cell lung cancer (NSCLC) who may benefit from treatment with IRESSA® (gefitinib), TAGRISSO® (osimertinib), and TARCEVA® (erlotinib). On October 26, 2020 the FoundationOne® Liquid CDx test was approved as a companion diagnostic for *BRCA1* and *BRCA2* alterations in epithelial ovarian cancer for patients who may benefit from treatment with RUBRACA® (rucaparib), *ALK* rearrangements in non-small cell lung cancer for patients who may benefit from treatment with ALECENSA® (alectinib), and *PIK3CA* mutations patients with breast cancer who may benefit from treatment with PIQRAY® (alpelisib). On November 6, 2020, the the FoundationOne® Liquid CDx test was approved as a companion diagnostic for *BRCA1*, *BRCA2* and *ATM* alterations in mCRPC patients who may benefit from treatment with LYNPARZA® (olaparib). The SSEDs to support the previously approved indications are available on the CDRH website. The current supplement was submitted to expand the indication for the FoundationOne® Liquid CDx test as a companion diagnostic for the indication listed in the table below. New Indication Being Sought in this PMA supplement submission. | Tumor Type | Biomarker(s) Detected | Therapy | | --- | --- | --- | | Non-small cell lung cancer (NSCLC) | *MET* single nucleotide variants (SNVs) and indels that lead to *MET* exon 14 skipping | TABRECTA® (capmatinib) | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 1 of 46 {1} ## II. INDICATIONS FOR USE FoundationOne® Liquid CDx is a qualitative next generation sequencing based in vitro diagnostic test that uses targeted high throughput hybridization-based capture technology to detect and report substitutions, insertions and deletions (indels) in 311 genes, including rearrangements in four (4) genes, and copy number alterations in three (3) genes. FoundationOne® Liquid CDx utilizes circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood of cancer patients collected in FoundationOne® Liquid CDx cfDNA blood collection tubes included in the FoundationOne® Liquid CDx Blood Sample Collection Kit. The test is intended to be used as a companion diagnostic to identify patients who may benefit from treatment with the targeted therapies listed in Table 1 in accordance with the approved therapeutic product labeling. **Table 1: Companion diagnostic indications** | Tumor Type | Biomarker(s) Detected | Therapy | | --- | --- | --- | | Non-small cell lung cancer (NSCLC) | *ALK* Rearrangements | ALECENSA® (alectinib) | | | *EGFR* Exon 19 deletions and *EGFR* Exon 21 L858R alteration | IRESSA® (gefitinib) TAGRISSO® (osimertinib) TARCEVA® (erlotinib) | | | *MET* single nucleotide variants (SNVs) and indels that lead to *MET* exon 14 skipping | TABRECTA® (capmatinib) | | Prostate cancer | *BRCA1, BRCA2, and ATM* alterations | LYNPARZA® (olaparib) | | | *BRCA1, BRCA2* alterations | RUBRACA® (rucaparib) | | Ovarian Cancer | *BRCA1, BRCA2* alterations | RUBRACA® (rucaparib) | | Breast Cancer | *PIK3CA* mutations C420R, E542K, E545A, E545D [1635G>T only], E545G, E545K, Q546E, Q546R, H1047L, H1047R, and H1047Y | PIQRAY® (alpelisib) | Additionally, FoundationOne® Liquid CDx is intended to provide tumor mutation profiling to be used by qualified health care professionals in accordance with professional guidelines in oncology for patients with solid malignant neoplasms. A negative result from a plasma specimen does not mean that the patient’s tumor is negative for genomic findings. Patients who are negative for the mutations listed in Table 1 should be reflexed to routine biopsy and their tumor mutation status confirmed using an FDA-approved tumor tissue test, if feasible. Genomic findings other than those listed in Table 1 of the intended use statement are not prescriptive or conclusive for labeled use of any specific therapeutic product. FoundationOne® Liquid CDx is a single-site assay performed at Foundation Medicine, Inc. in Cambridge, MA. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 2 of 46 {2} ### III. CONTRAINDICATIONS There are no known contraindications. ### IV. WARNINGS AND PRECAUTIONS - Alterations reported may include somatic (not inherited) or germline (inherited) alterations; however, the test does not distinguish between germline and somatic alterations. If a reported alteration is suspected to be germline, confirmatory testing should be considered in the appropriate clinical context. - The test is not intended to replace germline testing or to provide information about cancer predisposition. - Patients for whom no companion diagnostic alterations are detected should be considered for confirmation with an FDA-approve tumor tissue test, if possible. ### V. DEVICE DESCRIPTION The FoundationOne® Liquid CDx (F1LCDx) assay is performed exclusively as a laboratory service using circulating cell-free DNA (cfDNA) isolated from plasma derived from anti-coagulated peripheral whole blood from patients with solid malignant neoplasms. The assay employs a single DNA extraction method to obtain cfDNA from plasma from whole blood. Extracted cfDNA undergoes whole-genome shotgun library construction and hybridization-based capture of 324 cancer-related genes. All coding exons of 309 genes are targeted; select intronic or non-coding regions are targeted in three genes (refer to Table 2 for the complete list of genes reported by F1LCDx). Hybrid-capture selected libraries are sequenced with deep coverage using the NovaSeq 6000 platform. Sequence data are processed using a custom analysis pipeline designed to detect genomic alterations, including base substitutions and indels in 311 genes, copy number variants in three genes, and genomic rearrangements in four genes. A subset of targeted regions in 75 genes is baited for increased sensitivity. Table 2: Genomic Regions in which Variants are Reported by FoundationOne® Liquid¹ | **ABL1** *[Exons 4-9]* | *ACVR1B* | **AKT1** *[Exon 3]* | *AKT2* | *AKT3* | **ALK** *[Exons 20-29, Introns 18,19]* | *ALOX12B* | *AMER1* *(FAM123B)* | *APC* | *AR* | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | **ARAF** *[Exons 4, 5, 7, 11, 13, 15, 16]* | *ARFRP1* | *ARID1A* | *ASXL1* | *ATM* | *ATR* | *ATRX* | *AURKA* | *AURKB* | *AXIN1* | | *AXL* | *BAP1* | *BARD1* | *BCL2* | *BCL2L1* | *BCL2L2* | *BCL6* | *BCOR* | *BCORL1* | *BCR** *[Introns 8, 13, 14]* | | **BRAF** *[Exons 11-18, Introns 7-10]* | **BRCA1** *[Introns 2, 7, 8, 12, 16, 19, 20]* | **BRCA2** *[Intron 2]* | *BRD4* | *BRIP1* | *BTG1* | *BTG2* | **BTK** *[Exons 2, 15]* | *C11orf30* *(EMSY)* | *C17orf39* *(GID4)* | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 3 of 46 {3} | CALR | CARD11 | CASP8 | CBFB | CBL | CCND1 | CCND2 | CCND3 | CCNE1 | CD22 | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | CD70 | CD74* [Introns 6-8] | CD79A | CD79B | CD274 (PD-L1) | CDC73 | CDH1 | CDK12 | CDK4 | CDK6 | | CDK8 | CDKN1A | CDKN1B | CDKN2A | CDKN2B | CDKN2C | CEBPA | CHEK1 | CHEK2 | CIC | | CREBBP | CRKL | CSF1R | CSF3R | CTCF | CTNNA1 | CTNNB1 [Exon 3] | CUL3 | CUL4A | CXCR4 | | CYP17A1 | DAXX | DDR1 | DDR2 [Exons 5, 17, 18] | DIS3 | DNMT3A | DOT1L | EED | EGFR [Introns 7, 15, 24-27] | EP300 | | EPHA3 | EPHB1 | EPHB4 | ERBB2 | ERBB3 [Exons 3, 6, 7, 8, 10, 12, 20, 21, 23, 24, 25] | ERBB4 | ERCC4 | ERG | ERRF11 | ESR1 [Exons 4-8] | | ETV4* [Intron 8] | ETV5* [Introns 6, 7] | ETV6* [Introns 5, 6] | EWSR1* [Introns 7-13] | EZH2 [Exons 4, 16, 17, 18] | EZR* [Introns 9-11] | FAM46C | FANCA | FANCC | FANCG | | FANCL | FAS | FBXW7 | FGF10 | FGF12 | FGF14 | FGF19 | FGF23 | FGF3 | FGF4 | | FGF6 | FGFR1 [Introns 1, 5, Intron 17] | FGFR2 [Intron 1, Intron 17] | FGFR3 [Exons 7, 9 (alternative designation exon 10), 14, 18, Intron 17] | FGFR4 | FH | FLCN | FLT1 | FLT3 [Exons 14, 15, 20] | FOXL2 | | FUBP1 | GABRA6 | GATA3 | GATA4 | GATA6 | GNA11 [Exons 4, 5] | GNA13 | GNAQ [Exons 4, 5] | GNAS [Exons 1, 8] | GRM3 | | GSK3B | H3F3A | HDAC1 | HGF | HNF1A | HRAS [Exons 2, 3] | HSD3B1 | ID3 | IDH1 [Exon 4] | IDH2 [Exon 4] | | IGF1R | IKBKE | IKZF1 | INPP4B | IRF2 | IRF4 | IRS2 | JAK1 | JAK2 [Exon 14] | JAK3 [Exons 5, 11, 12, 13, 15, 16] | | JUN | KDM5A | KDM5C | KDM6A | KDR | KEAP1 | KEL | KIT [Exons 8, 9, 11, 12, 13, 17, Intron 16] | KLHL6 | KMT2A (MLL) [Introns 6, 8-11, Intron 7] | | KMT2D (MLL2) | KRAS | LTK | LYN | MAF | MAP2K1 (MEK1) [Exons 2, 3] | MAP2K2 (MEK2) [Exons 2-4, 6, 7] | MAP2K4 | MAP3K1 | MAP3K13 | | MAPK1 | MCL1 | MDM2 | MDM4 | MED12 | MEF2B | MEN1 | MERTK | MET | MITF | | MKNK1 | MLH1 | MPL[Exon 10] | MRE11A | MSH2 [Intron 5] | MSH3 | MSH6 | MST1R | MTAP | MTOR [Exons 19, 30, 39 40, 43-45, 47, 48, 53, 56] | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 4 of 46 {4} | MUTYH | MYB* [Intron 14] | MYC [Intron 1] | MYCL (MYCL1) | MYCN | MYD88 [Exon 4] | NBN | NF1 | NF2 | NFE2L2 | | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | | NFKBIA | NKX2-1 (TTF-1) | NOTCH1 | NOTCH2 [Intron 26] | NOTCH3 | NPM1 [Exons 4-6, 8, 10] | NRAS [Exons 2, 3] | NSD3 (WHSC1L1) | NT5C2 | NTRK1 [Exons 14,15, Introns 8-11] | | NTRK2 [Intron 12] | NTRK3 [Exons 16, 17] | NUTM1* [Intron 1] | P2RY8 | PALB2 | PARK2 | PARP1 | PARP2 | PARP3 | PAX5 | | PBRM1 | PDCD1 (PD-1) | PDCD1L G2 (PD-L2) | PDGFRA [Exons 12, 18, Introns 7, 9, 11] | PDGFRB [Exons 12- 21, 23] | PDK1 | PIK3C2B | PIK3C2G | PIK3CA [Exons 2, 3, 5-8, 10, 14, 19, 21 (Coding Exons 1, 2, 4- 7, 9, 13, 18, 20)] | PIK3CB | | PIK3R1 | PIM1 | PMS2 | POLD1 | POLE | PPARG | PPP2R1A | PPP2R2A | PRDM1 | PRKAR1A | | PRKCI | PTCH1 | PTEN | PTPN11 | PTPRO | QKI | RAC1 | RAD21 | RAD51 | RAD51B | | RAD51C | RAD51D | RAD52 | RAD54L | RAF1 [Exons 3, 4, 6, 7, 10, 14, 15, 17, Introns 4-8] | RARA [Intron 2] | RB1 | RBM10 | REL | RET [Introns 7, 8, Exons 11, 13-16, Introns 9-11] | | RICTOR | RNF43 | ROS1 [Exons 31, 36-38, 40, Introns 31- 35] | RPTOR | RSPO2* [Intron 1] | SDC4* [Intron 2] | SDHA | SDHB | SDHC | SDHD | | SETD2 | SF3B1 | SGK1 | SLC34A2* [Intron 4] | SMAD2 | SMAD4 | SMARCA4 | SMARCB1 | SMO | SNCAIP | | SOCS1 | SOX2 | SOX9 | SPEN | SPOP | SRC | STAG2 | STAT3 | STK11 (LKB1) | SUFU | | SYK | TBX3 | TEK | TERC* [ncRNA] | TERT* [Promoter] | TET2 | TGFBR2 | TIPARP | TMPRSS2* [Introns 1-3] | TNFAIP3 | | TNFRSF14 | TP53 | TSC1 | TSC2 | TYRO3 | U2AF1 | VEGFA | VHL | WHSC1 | WTI | | XPO1 | XRCC2 | ZNF217 | ZNF703 | | | | | | | ¹ As part of its FDA-approved intended use, the F1LCDx assay interrogates 324 genes, including 309 genes with complete exonic (coding) coverage and 15 genes with only select non-coding coverage (indicated with an *). Select genes and select exons (indicated in bold) are captured with increased sensitivity. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 5 of 46 {5} The reporting of rearrangements and copy number alterations are restricted to those genes included in Table 3, below. Table 3: Genes for which copy number alterations and rearrangements are reported for tumor profiling by F1LCDx | Alteration Type | Genes | | --- | --- | | Copy Number Alterations | BRCA1, BRCA2, ERBB2 | | Rearrangements | ALK, BRCA1, BRCA2 | The test report includes variants reported in the following levels: ### Level 1: Companion Diagnostics (CDx) Clinical evidence should be presented from a prospectively designed clinical trial. Results can also be presented from a retrospective clinical bridging study demonstrating that the clinical endpoints are preserved using plasma samples in trials where enrollment was based on tissue test results. For follow-on markers, a clinical concordance study demonstrating non-inferiority to the original FDA-approved cfDNA-based companion diagnostic device (refer to Li, Meijuan. Statistical Methods for Clinical Validation of Follow-On Companion Diagnostic Devices via an External Concordance Study. Statistics in Biopharmaceutical Research. 8: 35-363, 2016) is required. In addition to the clinical validation, analytical validation for each specific Level 1 CDx biomarker should be presented. ### Level 2: cfDNA Biomarkers With Strong Evidence of Clinical Significance in cfDNA For a Level 2 claim of cfDNA biomarkers with strong evidence of clinical significance, clinical validation needs to be from evidence presented with FDA-approved liquid biopsy companion diagnostic biomarkers for the specific tumor type at the biomarker or variant level. Such claims should also be supported by analytical performance for each biomarker from at least LoD, precision/ reproducibility, and accuracy studies. ### Level 3A: Biomarkers With Evidence of Clinical Significance in Tissue Supported by Strong Analytical Validation Using cfDNA and Concordance Between cfDNA and Tissue. Clinical evidence can be provided from tissuebased companion diagnostics. This should also be supported by analytical validation (LoD, precision, analytical accuracy, and concordance study to a tissue-based test) for the specific tumor type at the biomarker or variant level, using a representative approach for SNVs and indels. Evidence evaluating concordance between cfDNA- and tissue-samples for FDA-approved tissue markers should be demonstrated using an FDA-approved tissue test or a validated tissue test. ### Level 3B: Biomarkers With Evidence of Clinical Significance in Tissue Supported by Analytical Validation Using cfDNA Clinical evidence can be provided from tissue based companion diagnostics, with analytical validation supported by a representative approach for SNVs and indels from key analytical studies (such as LoD, accuracy, and precision). PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 6 of 46 {6} ## Level 4: Other Biomarkers With Potential Clinical Significance Biomarkers not categorized into Levels 1, 2, or 3 can be included under Level 4 for informational purposes or to be used to direct patients toward clinical trials for which they may be eligible. Such claims can be supported by clinical rationale for inclusion in the panel. Such rationale could also include peer-reviewed publications for genes/ variants in tissue, variant information from well curated public databases, or in vitro pre-clinical models. Analytical validation should be supported by a representative approach for SNVs and indels from key analytical studies (such as LoD, accuracy, and precision). ## FoundationOne® Liquid CDx cfDNA Blood Specimen Collection Kit Contents The test includes a blood specimen collection kit, which is sent to ordering laboratories. The shipping kit contains the following components: - Specimen preparation and shipping instructions - Two FoundationOne® Liquid CDx cfDNA Blood Collection Tubes (8.5 mL nominal fill volume per tube) - Return shipping label ## Instruments The F1LCDx assay is intended to be performed with the serial number-controlled instruments indicated in Table 5, below. All instruments are qualified by Foundation Medicine, Inc. (Foundation Medicine or FMI) under Foundation Medicine's Quality System. Table 5: Instruments for use with the F1LCDx assay | Instrument | | --- | | Illumina NovaSeq 6000 | | Beckman Biomek NXP Span-8 Liquid Handler | | Thermo Scientific Kingfisher Flex DW 96 | | Bravo Benchbot | | Hamilton STARlet STAR Liquid Handling Workstation | ## Test Process All assay reagents including blood collection tubes included in the F1LCDx assay process are qualified by Foundation Medicine and are compliant with the medical device Quality System Regulation (QSR). ### A. Specimen Collection and Preparation Whole blood specimens are collected in F1LCDx cfDNA Blood Collection Tubes (BCT) provided as a component of the F1LCDx specimen collection kit. Prior to cfDNA isolation, the plasma is separated from whole blood by centrifugation, which separates the plasma from the buffy coat (white blood cells) and red blood cells. The plasma layer is removed from the buffy coat to avoid contamination of cellular DNA into the plasma sample. A residual volume of plasma remains in the tube to avoid disturbing the buffy coat. A second spin of the separated plasma at high speed further pellets cell debris and protein. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 7 of 46 {7} ## B. DNA Extraction Following the separation of plasma from whole blood, cfDNA is isolated from plasma using the KingFisher™ Flex Magnetic Particle Processor, which uses an efficient and automated method to purify cfDNA. The KingFisher™ Instrument uses magnetic rods to move nucleic acid through purification phases of binding, washing, and elution to yield high purity cfDNA. After isolating cfDNA, the Agilent 4200 TapeStation is used to quantify cfDNA. ## C. Library Construction Library Construction (LC) begins with the normalization of cfDNA. The samples are purified, using AMPure XP Beads (Agencourt). Solid-phase reversible immobilization (SPRI) purification is used subsequent to library construction with the NEBNext kits (NEB), including mixes for end repair with blunt-end and 5'-phosphorylate the cfDNA fragments using T4 Polynucleotide Kinase and T4 DNA Polymerase. This step prepares the 3'- end for dA-addition while also preparing the 5'-end of the DNA fragment for ligation. Second, dA-addition will incorporate a single dAMP to the 3'-end of the End-Repaired material. After dA-addition, a universal Y-adaptor is ligated onto each end of the DNA fragment using a DNA ligase. These steps are performed in 96-well plates (Eppendorf) on a Bravo Benchbot (Agilent) using the "with-bead" protocol to maximize reproducibility and library yield. Indexed (Foundation Medicine customized six base pair barcodes) sequencing libraries are PCR amplified with a high-fidelity DNA polymerase (HiFi™, Kapa) for ten cycles, SPRI purified and quantified by PicoGreen fluorescence assay (Invitrogen). Process matched control (PMC) is prepared and added to the plate with other cfDNA samples at the beginning of LC. ## D. Hybrid Capture Hybrid Capture begins with the normalization of each library from 500 ng to 2000 ng. Solution hybridization is performed using a >50-fold molar excess of a pool of individually synthesized 5'-biotinylated DNA 120 base pair oligonucleotides (Integrated DNA Technology) for baits. The baits target regions from 324 cancer-related genes including all coding exons of 309 genes and only select introns or non-coding regions in 15 genes. Baits were designed by appointing overlapping 120 bp DNA sequence intervals covering target exons (60 bp overlap) and introns (20 bp overlap), with a minimum of three baits per target; single nucleotide polymorphism (SNP) targets were allocated one bait each. Intronic baits were filtered for repetitive elements as defined by the University of California at Santa Cruz (UCSC) Genome Repeat Masker track. Hybrid selection of targets demonstrating reproducibly low coverage was boosted by increasing the number of baits for these targets. Upon completion of the pre-capture normalization, blocking DNA (adaptor block, Cot, Salmon Sperm DNA) is added to the sequencing library and the mixture is lyophilized in a 96-well plate. The library is then re-suspended in nuclease-free water, heat denatured at 95°C for 5 minutes, temperature ramps from 95°C to 68°C to anneal blocking DNA, and then the samples are incubated at 68°C for a minimum of 5 minutes before the addition of the bait set reagent. After a 20-24-hour PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 8 of 46 {8} incubation, the library-bait duplexes are captured on paramagnetic MyOne™ streptavidin beads (Invitrogen) and off-target library is removed by washing one time with Saline Sodium Citrate (SSC) at 25°C and four times with SSC at 55°C. The PCR master mix is added to directly amplify the captured library from the washed beads. After amplification, the samples are SPRI purified and quantified by PicoGreen. ### E. Sequencing Sequencing on the Illumina NovaSeq 6000 platform employs on-board cluster generation (OBCG) using patterned flow cell (FC) technology to generate monoclonal clusters via ExAmp from a single DNA template. The clusters are then sequenced using sequencing by synthesis (SBS) chemistry. The NovaSeq system is capable of sequencing up to two flow cells at a time. During OBCG, a single DNA template is introduced into each of the primer substrate layered nanowells of the flow cell, where the template is immediately and rapidly amplified by ExAmp. This rapid amplification prevents other DNA templates from binding, ensuring a monoclonal cluster is formed in each nanowell. The procedure allows for fixed size and spacing of the clusters which results in improved and more accurate resolution. A growing nucleotide chain is created on the flow cell by incorporating fluorescently labeled, 3'-blocked dNTPs. After excitation by a laser, the camera captures the emission color of the incorporated, fluorescently labeled nucleotide. The 3'-block is then removed, reverting the nucleotide to its natural form, which allows the polymerase to add another base to the growing double strand of DNA. With each successive SBS cycle, a new fluorescently labeled 3'- blocked dNTP is added. SBS allows for millions of discrete clusters of clonal copies of DNA to be sequenced in parallel. ### F. Sequence Analysis Sequence data are analyzed using mainly proprietary software developed by Foundation Medicine. External tools used include: 1) BWA (Burrows-Wheeler Aligner) v0.7.17, for aligning sequence reads to the genomic reference, 2) Samtools v1.6 for utility operations, 3) Picard tools v1.56 for metrics calculations, and 4) Biopython for the pairwise2 sequence alignment module. Reads from each Illumina flow cell are demultiplexed (sorted into sets of reads deriving from distinct samples), and their fragment barcodes (FBCs) are extracted and encoded into the read names. For each sample, read pairs with matching, valid FBCs are aligned and processed together to: 1) identify clusters of reads originating from the same original fragment; 2) merge overlapping read pairs into single reads, where possible; and 3) generate consensus reads representing all information in the set of reads for each cluster, encoding positions with mismatches (errors) with base quality 20. The consensus reads are then aligned to the reference genome to generate the 'consensus' BAM. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 9 of 46 {9} For the detection of short variants (e.g., substitutions and small indels) in each target region of interest, a de novo assembly is performed. This is done using proprietary software to generate a de Bruijn graph including all k-mers in reads mapping to a particular locus. The graph is parsed to identify paths that originate and terminate in reference nodes from the locus. Increased k-mer sizes may be used to account for ambiguities, cycles, and other problematic regions within the graph. The result of the graph traversal is a set of candidate variants. For each variant, there is a set of k-mers supporting the variant and a set of k-mers that would support the reference or another variant at the location. Each candidate variant is then scanned against reads in the locus to identify which reads support either the candidate variant or a different variant or reference at the location. The cluster membership of the supporting reads is then assessed to determine which clusters show unambiguous support for the variant and which have conflicting assignments, indicating that the variant may have arisen as an error in sequencing or library preparation. The final variant calls are made based on a model that takes into account the coverage at the location, the number of supporting read clusters and their redundancy level, and the number of error-containing clusters. ### G. Report Generation Approved results are annotated by automated software with CDx relevant information and are merged with patient demographic information and any additional information provided by Foundation Medicine as a professional service prior to approval and release by the laboratory director or designee. ### H. Internal Process Controls #### Positive Control Each assay run includes a control sample run in duplicate. The control sample contains a pool of eleven HapMap cell lines and is used as a positive mutation detection control. 100 different germline SNPs present across the entire targeted region are required to be detected by the analysis pipeline. #### Sensitivity Control The HapMap control pool used as the positive control is prepared to contain variants at 0.1%, 10% mutant allele frequency (MAF) which must be detected by the analysis pipeline to ensure expected sensitivity for each run. #### Negative Control Samples are barcoded molecularly at the library construction (LC) stage. Only reads with a perfect molecular barcode sequence are incorporated into the analysis. The Analysis Pipeline includes an algorithm that analyzes the SNP profile of each specimen to identify potential contamination that may have occurred prior to molecular barcoding. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 10 of 46 {10} # I. CDx Classification Criteria 1. BRCA1 and BRCA2 alterations to identify patients eligible for rucaparib in prostate and ovarian cancer: The CDx classification criteria and the list of BRCA1/BRCA2 missense mutations for rucaparib, based on the trial prespecifications are described in Table 5 and Table 6; however, not all the missense mutations listed below were observed in the TRITON2, ARIEL2, and PROfound clinical studies. Table 5: Classification Criteria for Deleterious Tumor BRCA Variants | Qualification Criteria | Sequence Classification | Methodology | | --- | --- | --- | | A BRCA1 or BRCA2 alteration that includes any of the sequence classifications | Protein truncating mutations | Sequence analysis identifies premature stop codons anywhere in the gene coding region, except: 3' of and including BRCA2 K3326* | | | Splice site mutations | Sequence analysis identifies variant splice sequences at intron/exon junctions -/+ 2bp of exon starts/ends | | | Homozygous deletions | Sequence analysis identifies deletions in both gene alleles of ≥1 exon in size | | | Large protein truncating rearrangements | Sequence analysis identifies protein truncating rearrangements | | | Deleterious missense mutations | Curated list | Table 6: Deleterious BRCA Missense Alterations in rucaparib | BRCA1 Alterations (Protein Change) | | | | | BRCA2 Alterations (Protein Change) | | | | --- | --- | --- | --- | --- | --- | --- | --- | | M1V | C44Y | R71T | R1699W | G1770V | M1V | R2336P | T2722R | | M1T | C44F | R71M | R1699Q | M1775K | M1T | R2336L | D2723H | | M1R | C47S | S770L | G1706R | M1775R | M1R | R2336H | D2723G | | M1I | C47Y | R1495T | G1706E | C1787S | M1I | T2412I | G2724W | | M18T | C47F | R1495M | A1708E | G1788V | D23N | R2602T | G2748D | | L22S | C61S | R1495K | S1715R | P1812A | D23Y | W2626C | A2911E | | I26N | C61G | E1559K | S1722F | A1823T | S142N | I2627F | E3002K | | T37K | C61Y | E1559Q | V1736A | V1833M | S142I | R2659T | R3052W | | C39R | C64R | T1685A | G1738R | W1837R | V159M | R2659K | D3095G | | C39G | C64G | T1685I | G1738E | V1838E | V211I | E2663V | D3095E | | C39Y | C64Y | D1692N | K1759N | | V211L | S2670L | N3124I | | C39W | C64W | M1689R | L1764P | | Y600C | I2675V | N3187K | | H41R | R71G | D1692H | I1766N | | K1530N | T2722K | | | C44S | R71K | D1692Y | I1766S | | | | | 2. ATM, BRCA1 and BRCA2 alterations to identify patients eligible for olaparib in mCRPC: Table 7: Rules Applied to the Aforementioned Genes: PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 11 of 46 {11} | Qualification Criteria | Sequence Classification | Methodology | Comments | | --- | --- | --- | --- | | A gene alteration that includes any of the sequence classifications | Protein truncating mutations | Sequence analysis identifies premature stop codons anywhere in the gene coding region, except: 3' of and including *BRCA2* K3326* | Does not include VUS. Includes mutations on the canonical transcript only for genes *ATM*, *BRCA1*, and *BRCA2*. | | | Splice site mutations | Sequence analysis identifies variant splice sequences at intron/exon junctions -/+ 2bp of exon starts/ends | Does not include VUS. Includes indels that extend through ±2bp from the intron/exon junction. Includes mutations on the canonical transcript only for genes *ATM*, *BRCA1*, and *BRCA2*. | | | Homozygous deletions | Sequence analysis identifies deletions in both gene alleles of ≥1 exon in size | Does not include VUS Only reported for *BRCA1*&2. Not reported for *ATM*. | | | Large protein truncating rearrangements | Sequence analysis identifies protein truncating rearrangements | Does not include VUS | | | Deleterious missense mutations | Curated list | Protein effects from list of missense mutations on the canonical transcript only for genes *ATM*, *BRCA1*, and *BRCA2*. | Alterations reported are limited to those within the alteration-calling capabilities of FMI as of March 2, 2020. ATM missense mutations were identified from the ClinVar database. Should the calling capabilities expand, additional alterations that meet the above criteria may also be reported, per FDA approval **Table 8. List of Deleterious Missense Mutations by Protein Effect, Implemented on the Respective Canonical Transcript.** | *BRCA1* | | *BRCA2* | | *ATM* | | | --- | --- | --- | --- | --- | --- | | Protein Effect (PE) | FMI Annotated PE | Protein Effect (PE) | FMI Annotated PE | Protein Effect (PE) | FMI Annotated PE | | MIV | MIV | MIR | MIR | MIT | MIT | | MII | MII | MII | MII | R2032K | R2032K | | C6IG | C6IG | VI59M | VI59M | R2227C | R2227C | | C64Y | C64Y | V211L | V211L | R2547 S2549del | R2547 S2549del | | R7IG | R7IG | V211I | V211I | G2765S | G2765S | | R7IK | R7IK | R2336P | R2336P | R2832C | R2832C | | RI495M | RI495M | R2336H | R2336H | S2855 V2856delinsR1 | S2855 V2856delinsR1 S2855 V2856>R1 | | EI559K | EI559K | | | R3008C | R3008C | | DI692N | DI692N | | | R3008H | R3008H | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 12 of 46 {12} | BRCA1 | | BRCA2 | | ATM | | | --- | --- | --- | --- | --- | --- | | Protein Effect (PE) | FMI Annotated PE | Protein Effect (PE) | FMI Annotated PE | Protein Effect (PE) | FMI Annotated PE | | DI692H | DI692H | | | [VUS from Jan 2016 HRR* List to be Excluded] | | | RI699W | RI699W | | | V2424G | V2424G | | AI708E | AI708E | | | [Excluded from Jan 2016 HRR List] | | | G1788V | G1788V | | | K750K | splice site 2250G>A | HRR = Homologous Recombination Repair genes # Intronic Variants | Gene | Chr | Position | Ref | Alt | dbSNP | FMI Protein Effect | | --- | --- | --- | --- | --- | --- | --- | | ATM | chr11 | 108128198 | T | G | rs730881346 | [Variant Not Called by FMI] | | ATM | chr11 | 108214102 | AGTGA | A | rs730881295 | splice site 8418+5_8418+8delGTGA or splice site 8418+1_8418+4delGTGA | 3. CDx classification criteria for EGFR alterations: - Base substitutions resulting in EGFR L858R - In-frame deletions occurring within EGFR Exon 19 4. ALK rearrangements to identify patients eligible for treatment with ALECENSA® (alectinib): CDx positivity for an ALK rearrangement is based on the following variant classification criteria: - The ALK rearrangement must have pathogenic driver status (FMI driver status of "known" or "likely") - AND the disease type must be NSCLC - AND one of the following two conditions must hold: 1. The partner gene is EML4, or 2. The ALK breakpoint occurs within ALK intron 19 5. SNVs and indels that lead to MET exon 14 skipping to identify patients eligible for treatment with TABRECTA® (capmatinib). A SNV or indel in MET shall be considered to result in skipping of exon 14 if one or more of the following criteria are met: 1. Deletions greater than or equal to 5 bp that affect positions -3 to -30 in the intronic region immediately adjacent to the splice acceptor site at the 5' boundary of MET exon 14. 2. Indels affecting positions -1 or -2 at the splice acceptor site of the 5' boundary of MET exon 14. 3. Base substitutions and indels affecting positions 0, +1, +2, or +3 at the splice donor site of the 3' boundary of MET exon 14. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 13 of 46 {13} ## VI. ALTERNATIVE PRACTICES AND PROCEDURES There are FDA-approved companion diagnostic (CDx) alternatives for the detection of genetic alterations using cfDNA isolated from plasma samples, as listed in Table 1 of the F1LCDx intended use statement. The approved CDx tests are listed in Table 9, below; for additional details see FDA List of Cleared or Approved Companion Diagnostic Devices at: https://www.fda.gov/media/119249/download. Each alternative has its own advantages and disadvantages. A patient should fully discuss these alternatives with his/her physician to select the method that best meets expectations and lifestyle. **Table 9: FDA-approved companion diagnostic (CDx) alternatives** | Biomarker(s) Detected | Device | Company | Technology | Therapy | Indication | | --- | --- | --- | --- | --- | --- | | *EGFR* Exon 19 deletions and L858R Substitution Mutation | **cobas***EGFR* Mutation Test v2 | Roche Molecular Systems, Inc. | Polymerase Chain Reaction (PCR) | TARCEVA® (erlotinib), TAGRISSO® (osimertinib), and IRESSA® (gefitinib) | NSCLC | | | Guardant360 CDx | Guardant Health, Inc. | NGS | TAGRISSO® (osimertinib) | | | | | | | | | | *PIK3CA*: C420R, E542K, E545A, E545D [1635G>T only], E545G, E545K, Q546E, Q546R, H1047L, H1047R, and H1047Y | *therascreen PIK3CA* RGQ PCR test | QIAGEN, Inc. | PCR | PIQRAY® (alpelisib) | Breast Cancer | There are no FDA-approved CDx alternatives using cfDNA isolated from plasma for the detection of genomic alterations of *BRCA1*, *BRCA2*, and *ATM* for the identification of mCRPC patients eligible for treatment with LYNPARZA® (olaparib). There are no FDA-approved CDx alternatives using cfDNA isolated from plasma for the detection of genomic alterations of SNVs and indels that lead to *MET* exon 14 skipping to identify patients eligible for treatment with TABRECTA® (capmatinib). ## VII. MARKETING HISTORY Foundation Medicine designed and developed F1LCDx based on previous versions of the assay, including the FoundationACT (FACT) and FoundationOne® Liquid laboratory developed test (LDT), a revised version of FACT. The first commercial sample was tested in 2016. The FACT and FoundationOne® Liquid LDT have been used to detect the presence of genomic alterations in blood and plasma specimens. Neither the FACT nor FoundationOne® Liquid LDT were FDA-cleared or -approved. The F1LCDx assay was approved on August 26, 2020 for the detection of genomic alterations of *BRCA1* and *BRCA2* for the identification of mCRPC patients eligible for treatment with RUBRACA® (rucaparib) and the detection of *EGFR* Exon 19 deletions (Exon 19del) and L858R substitutions in plasma obtained from patients with advanced PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 14 of 46 {14} and metastatic NSCLC for treatment with TARCEVA® (erlotinib), TAGRISSO® (osimertinib), and IRESSA® (gefitinib). The F1LCDx assay was also approved for tumor mutation profiling for substitutions and indels to be used by qualified health care professionals in accordance with professional guidelines in oncology for patients with solid malignant neoplasms. The F1LCDx assay was approved on October 26, 2020 as a companion diagnostic for *BRCA1* and *BRCA2* alterations in epithelial ovarian cancer for patients who may benefit from treatment with RUBRACA® (rucaparib), *ALK* rearrangements in NSCLC for patients who may benefit from treatment with ALECENSA® (alectinib), and *PIK3CA* mutations in patients with breast cancer who may benefit from treatment with PIQRAY® (alpelisib). The October 26, 2020 approval also included the addition of rearrangements in three (3) genes, and copy number alterations in three (3) genes for tumor profiling. F1LCDx assay was approved on November 6, 2020 as a companion diagnostic for *BRCA1*, *BRCA2* and *ATM* for the identification of mCRPC patients eligible for treatment with LYNPARZA® (olaparib). The F1LCDx assay has been marketed in the United States, the European Union, and in several other foreign countries since August 2020. ### VIII. POTENTIAL ADVERSE EFFECTS OF THE DEVICE ON HEALTH Failure of the device to perform as expected or failure to correctly interpret test results may lead to incorrect F1LCDx assay results, and subsequently, inappropriate patient management decisions. Patients with false positive CDx biomarker results may undergo treatment with one of the therapies listed in the intended use statement without clinical benefit and may experience adverse reactions associated with the therapy. Patients with false negative results may not be considered for treatment with the indicated targeted therapy. There is also a risk of delayed results, which may lead to delay of treatment with the indicated therapy. For the specific adverse events related to the approved therapeutics, please see approved drug product labels. For the specific adverse events that occurred in the clinical study, please see the FDA approved package inserts for TABRECTA® (capmatinib) which is available at Drugs@FDA. ### IX. SUMMARY OF NONCLINICAL STUDIES #### A. Laboratory Studies The evidence in support of the analytical performance of F1LCDx in detecting SNVs and indels that lead to *MET* exon 14 skipping is presented in this section. Analytical accuracy/concordance and precision near the limit of detection (LoD) studies were conducted to support the indication for SNVs and indels that lead to *MET* exon 14 skipping using clinical samples. For F1LCDx platform-level validation (P190032), due to the lack of sufficient volume of clinical specimens, analytical performance characteristics were established for some of the studies using contrived samples, which consisted of enzymatically sheared cell ---PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 15 of 46 {15} line DNA spiked into human plasma and diluted with cfDNA isolated from healthy donor plasma. A contrived sample functional characterization (CSFC) study (Section IX.A.1) was conducted to demonstrate comparable performance of sheared cell line DNA samples as compared to cfDNA isolated from plasma specimens obtained from cancer positive patient specimens. Clinical specimens were used to assess analytical accuracy, precision and confirmation of the estimated limit of detection (LoD), and evaluate sample stability. For information regarding the platform-level validation, refer to Section IX.A. in Summary of Safety and Effectiveness Data P190032. ### 1. Analytical Accuracy/Concordance An analytical accuracy/concordance study was performed to demonstrate the concordance between F1LCDx and an externally validated NGS assay (evNGS) for the detection of SNVs and indels that lead to MET exon 14 skipping. Overall, there were 74 overlapping genes between the two assays and the evNGS bait set regions included the biomarker classification criteria for alterations that lead to MET exon 14 skipping. The comparison between short variants, including base substitutions and indels, detected by F1LCDx and the evNGS was evaluated for alterations leading to MET exon 14 skipping. For this study, 45 samples were selected from patients enrolled in the TABRECTA trial GEOMETRY-mono 1 study conducted to support the effectiveness of the device (refer to to Section X below). Additional 100 NSCLC samples were sourced from FMI's clinical archives, 38 samples from NSCLC patients previously evaluated in the accuracy study to support the original PMA P190032 (refer to section IX.A.2. in the SSED for the original PMA P190032), and 31 externally sourced plasma samples from NSCLC cases whose tissue specimens tested positive for MET exon 14 skipping alterations and were subsequently tested with F1LCDx to determine their MET exon 14 skipping associated alteration status prior to conducting the accuracy study statistical analysis. Samples selected from FMI's clinical archives that were positive for MET exon 14 skipping alterations were required to have a variant allele frequency (VAF) greater than or equal 0.40%. Of the 214 samples, 179 samples had DNA yield that allowed processing with F1LCDx at the specified LC DNA input of 30ng – 80ng. Thirty-five (35) samples were tested with F1LCDx at out of specification of 20ng – <30ng LC DNA input. Of the 179 samples that had sufficient DNA yield for testing with F1LCDx, 3 samples had a F1LCDx sequence analysis QC failure, while 4 had an evNGS QC failure. Analytical concordance using the evNGS assay results as the reference for the 172 samples that passed QC with both assays was determined. Forty-eight (48) of the 172 samples were identified as positive for MET exon 14 skipping alterations by F1LCDx. The statistical analysis using the evNGS assay results as the reference showed a positive percent agreement (PPA) of 94.87% with 95% CI (83.11%- PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 16 of 46 {16} 98.58%), a negative percent agreement (NPA) of 91.83% with 95% CI (85.80%, 95.32%), a positive predictive value (PPV) of 77.08% with 95% CI (63.46%, 86.69%) and a negative predictive value (NPV) of 98.39% with 95% CI (94.31%, 99.56%) as shown in Table 10, below. Since the samples were selected from different sources based on different assays, the unadjusted PPA/NPA and unadjusted PPV/NPV in Table 10 may be subject to potential bias. Table 10. Concordance Analysis Comparing Sample-level Biomarker Detection between F1LCDx and evNGS | | evNGS | | | | | | --- | --- | --- | --- | --- | --- | | | | MET ex14 positive | MET ex14 negative | Total | PPV/NPV (95% CI) | | F1LCDx | MET ex14 positive | 37 | 11 | 48 | PPV: 77.08% (63.46%, 86.69%) | | | MET ex14 Negative | 2 | 122 | 124 | NPV: 98.39% (94.31%, 99.56%) | | | Total | 39 | 133 | 172 | | | | PPA/NPA (95% CI) | PPA: 94.87% (83.11%, 98.58%) | NPA: 91.83% (85.80%, 95.32%) | | | Ten (10) of the eleven (11) samples that were F1LCDx-positive/evNGS-negative [F1LCDx(+)/evNGS(-)] were discordant due to differences in variant reporting by assays. Of the 11 samples, 10 samples harbored MET exon 14 deletions ≥6bp detectable by the evNGS variant caller, which calls variants including indels ≥6bp in MET exon 14 that are also included in the evNGS's loci of interest (LOI). Following variant calling, variant filtering is performed prior to reporting. The default setting of the evNGS analysis software filters out variants that are not present in the assay's LOI list and/or not annotated in public databases such as COSMIC, TCGA and dbSNP. Since MET ex14 indels ≥6bp are not part of the evNGS's LOI, this variant type is filtered out and not reported by the evNGS's analysis software in the default setting, and thus are considered negatives by the evNGS comparator assay. Further the remaining one (1) sample from the 11 samples that were F1LCDx (+)/evNGS(-), contained a MET exon 14 deletion <6bp which cannot be called with the evNGS variant caller regardless of the VAF level (i.e., this type of variant is "un-callable" not because of the sensitivity and specificity of the evNGS variant caller but because the variant caller can only output MET exon 14 deletions ≥6bp. In the two (2) discordant samples that were F1LCDx negative(-)/evNGS(+), base substitutions reported by the evNGS were not detected in the variant analysis pipeline of F1LCDx. These 2 discordances seem to stem from the low frequency of the variants, 0.47% and 0.54% VAF, which are close to the LoD of F1LCDx. Four (4) of the eleven (11) discordant samples that were F1LCDx(+)/evNGS(-) were from patients evaluated in the clinical therapeutic study for whom efficacy data was available. Of these 4 patients, 3 had partial response to TABRECTA, while one had progressive disease. Although these patients had discordant results, PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 17 of 46 {17} these results appear to suggest that these patient with F1LCDx(+)/evNGS(-) were MET exon 14 deletion positive. All of 37 samples that were F1LCDx(+)/evNGS(+) had MET exon 14 skipping alterations that correspond to biomarker rule category 3, i.e., these samples had base substitutions and indels affecting positions 0, +1, +2, or +3 at the splice donor site of the 3' boundary of MET exon 14. Therefore, samples representative of all three biomarker classification rules were not represented in the accuracy study. Although not called by evNGS comparator as positive due to variant filtering rules, 4 of the 11 F1LCDx(+)/evNGS(-) had MET exon 14 skipping alterations that correspond to biomarker rule category 1, and 3 out of 11 had MET exon 14 skipping alterations that correspond to biomarker rule category 1 and 2. The remaining 3 out of the 11 F1LCDx(+)/evNGS(-) samples that had biomarker rule category 3 MET exon 14 skipping alterations. These 10 samples were 100 % concordant at the variant level, i.e., these 10 samples were detected by evNGS, but were not reported due to variant filtering as described above. As samples that were selected for evaluation from FMI's clinical archives that were positive for MET exon 14 skipping alterations were required to have a VAF ≥0.40%, and since the lowest VAF test result observed in the accuracy study for the F1LCDx was 0.34% VAF for base substitutions and 0.73% VAF for indels, the accuracy of F1LCDx was not demonstrated for samples with variants below these VAF levels. A limitation addressing the uncertainty of the accuracy of MET exon 14 skipping alteration with VAFs below those evaluated in the accuracy is included as a limitation to the device (also refer to Section XII. C. below). ## 2. Analytical Sensitivity a. Limit of Blank (LoB) See Summary of Safety and Effectiveness Data for P190032. b. Limit of Detection (LoD) The LoD of a MET exon 14 indel in a contrived sample was evaluated as part of the LoD study for PMA P190032 (refer to Section IX.A.3.b) in the original SSED). The MET indel was determined to have an estimated LoD of 0.41% VAF using the empirical hit rate approach. Although this variant (splice site 3029-1G>T) did not meet the TABRECTA CDx biomarker definition, the LoD estimated using this indel variant was used for the confirmation of LoD study (see Section IX.A.2.c., below) due to availability of MET exon 14 skipping alteration indel positive samples. The LoD for a MET exon 14 skipping base substitution alteration was extrapolated from the median LoD from all the substitutions in the narrow high region in the F1 Liquid CDx platform and thus was estimated as 0.49% VAF. c. LoD Confirmation PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 18 of 46 {18} The two estimated LoD values for *MET* exon 14 skipping indels and base substitutions were used to confirm the LoD of *MET* exon 14 skipping alterations that meet the TABRECTA CDx biomarker definition. A total of three (3) clinical samples that harbored SNVs or indels that lead to *MET* exon 14 skipping were assessed in a confirmation of LoD study by F1LCDx. The SNVs evaluated correspond to the biomarker rule category 3, while the indel evaluated corresponds to the biomarker rule 1 and 2. The LoD values for *MET* exon 14 alterations were confirmed from the data generated in this study using one clinical cfDNA sample positive for a *MET* exon14 indel and two clinical cfDNA samples positive for *MET* exon14 base substitutions per *MET* exon 14 biomarker definition based on a hit rate of least 95%. In this study LoD was confirmed by testing 24 replicate measurements. The LoD for *MET* exon 14 indels is confirmed for a as the median VAF of 0.28% and the LoD for *MET* exon 14 SNVs is established as the median VAF of 0.40%, see Table 11. **Table 11: Summary of Confirmed LoD for SNVs and indels that lead to *MET* exon 14 skipping** | Targeted %VAF^{1,4} | Alteration Type | *MET* exon 14 Skipping Alteration | Previously Established LoD VAF^{2,3,4} | Mean VAF Calculated^{4} | Concordant/ Total (n/N) | Hit Rate 95%CI (%) | | --- | --- | --- | --- | --- | --- | --- | | 0.50% | Indel | *MET* exon14 splice site 2888-35 2889>A | 0.41%^{2} | 0.28% | 23/24 | 95.8% (79.8%, 99.3%) | | 0.50% | SNV | *MET* exon14 splice site 3028+1G>T | 0.49%^{3} | 0.45% | 23/24 | 95.8% (79.8%, 99.3%) | | 0.50% | SNV | *MET* exon14 splice site 3028+2T>C | 0.49%^{3} | 0.35% | 22/23 | 95.7% 79.0%, 99.2%) | $^{1}$ For samples processed in this study, 0.50% VAF represents 1 - 1.5x LoD. $^{2}$ LoD for *MET* Indels were estimated within the LoD Study in the original PMA P190032 (refer to Section IX.A.3.b ) $^{3}$ LoD established from platform subs in the narrow-high region within the LoD Study in the original PMA P190032 (refer to Section IX.A.3.b ) $^{4}$ The accuracy of %VAF has not been analytically validated See Section IX.A.7 of Summary of Safety and Effectiveness Data for P190032 for additional analytical sensitivity data. ### 3. Analytical Specificity: #### a. Potentially Interfering Substances: See Summary of Safety and Effectiveness Data for P190032. #### b. Hybrid Capture Bait Specificity: See Summary of Safety and Effectiveness Data for P190032. #### c. Carryover/Cross-Contamination: PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 19 of 46 {19} See Summary of Safety and Effectiveness Data for P190032. #### 4. Precision: a. Repeatability and Within-laboratory Reproducibility A precision study was conducted using five NSCLC samples harboring SNVs or indels that lead to MET exon 14 skipping covering all categories of the MET exon 14 biomarker rule. Repeatability including intra-run performance (run on the same plate under the same conditions) and reproducibility including inter-run performance (run on different plates under different conditions) were assessed and compared across three different sequencers and two different reagent lots, across multiple days of performance by multiple operators. The results for the precision study for the NSCLC samples near LoD are summarized in Tables 12 and 13, below. Table 12: Reproducibility results for SNVs and indels that lead to MET exon 14 skipping | Source Sample | Targeted VAF^{1} | MET exon 14 Alteration | Alteration Type | Concordant/ Total (n/N) | Reproducibility 95% CI (%)^{2} | Mean VAF Calculated^{1} | Fold LoD | | --- | --- | --- | --- | --- | --- | --- | --- | | 1 | 0.50% | MET exon14 splice site 2888-35_2889>A | Indel | 23/24 | 95.8% (79.8%, 99.3%) | 0.28% | 1.00X | | 2 | 0.50% | MET exon14 splice site 3028+1G>T | SNV | 23/24 | 95.8% (79.8%, 99.3%) | 0.45% | 1.13X | | 2 | 1.00% | MET exon14 splice site 3028+1G>T | SNV | 23/23 | 100.% (85.7%, 100%) | 0.85% | 2.13X | | 3 | 0.50% | MET exon14 splice site 3028+2T>C | SNV | 22/23 | 95.7% (79.0%, 99.2%) | 0.35% | 0.88X | | 3 | 1.00% | MET exon14 splice site 3028+2T>C | SNV | 24/24 | 100% (86.2%, 100%) | 0.76% | 1.90X | | 4 | 0.96% | MET exon14 splice site 2888-17_2888-3del15 | Indel | 24/24 | 100% (86.2%, 100%) | 1.17% | 4.18X | | 5 | 1.30% | MET exon 14 splice site 3005_3028+3>C | Indel | 24/24 | 100% (86.2%, 100%) | 1.67% | 5.96X | $^{1}$ Quantitative reporting of %VAF/%TF has not been approved by FDA. $^{2}$ The 95% CIs were calculated using the Wilson Method Table 13: Repeatability results for SNVs and indels that lead to MET exon 14 skipping PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 20 of 46 {20} | Source Sample | Targeted VAF^{1} | MET exon 14 Alteration | Alteration Type | Concordant / Total (n/N) | Repeatability 95% CI (%) | Mean VAF Calculated^{1} | Fold LoD | | --- | --- | --- | --- | --- | --- | --- | --- | | 1 | 0.50% | MET exon14 splice site 2888-35_2889>A | Indel | 11/12 | 91.7% (64.6%, 98.5%) | 0.28% | 1.00X | | 2 | 0.50% | MET exon14 splice site 3028+1G>T | SNV | 11/12 | 91.7% (64.6%, 98.5%) | 0.45% | 1.13X | | 2 | 1.00% | MET exon14 splice site 3028+1G>T | SNV | 11/11 | 100% (74.1%, 100%) | 0.85% | 2.13X | | 3 | 0.50% | MET exon14 splice site 3028+2T>C | SNV | 10/11 | 90.9% (62.3%, 98.4%) | 0.35% | 0.88X | | 3 | 1.00% | MET exon14 splice site 3028+2T>C | SNV | 12/12 | 100% (75.8%, 100%) | 0.76% | 1.90X | | 4 | 0.96% | MET exon14 splice site 2888-17_2888-3del15 | Indel | 12/12 | 100% (75.8%, 100%) | 1.17% | 4.18X | | 5 | 1.30% | MET exon 14 splice site 3005_3028+3>C | Indel | 12/12 | 100% (75.8%, 100%) | 1.67% | 5.96X | $^{1}$ Quantitative reporting of %VAF/%TF has not been approved by FDA. $^{2}$ The 95% CIs were calculated using the Wilson Method Inter-run reproducibility was evaluated across 24 replicates and intra-run repeatability was evaluated across 12 duplicates per plate. Three replicates exhibited discordances due to low coverage and low detected allele frequency, which was below pipeline reporting thresholds. Overall, the reproducibility was established as 98.2% and the repeatability was established at 96.3%. The corresponding two-sided Wilson score 95% CIs are provided for repeatability and reproducibility positive call rates. b. Tumor Mutation Profiling Variants: See Summary of Safety and Effectiveness Data for P190032 and P200006 and Section XIII. c. Reagent Lot-to-Lot Reproducibility: See Summary of Safety and Effectiveness Data for P190032. d. Instrument-to-Instrument Reproducibility: See Summary of Safety and Effectiveness Data for P190032. e. Reagent Lot Interchangeability: See Summary of Safety and Effectiveness Data for P190032. f. Curator Precision: See Summary of Safety and Effectiveness Data for P190032. ### 5. Comparability Across Cancer Types: See Summary of Safety and Effectiveness Data for P190032 and P200006. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 21 of 46 {21} ## 6. Stability: ### a. Reagent Stability: The reagent stability of F1LCDx assay was assessed by analyzing data from each of eight samples in triplicate, per each of three different lots of LC, HC, and sequencing reagents. A total of nine analyses for each specimen were completed for each of six time points assessed. A total of 72 tests were assessed per time period; a total of 432 samples and six time points (one baseline timepoint and 5 subsequent experimental timepoints) were included in this study overall. Each of the three sample Master Library Pools (MPLs), representing three LC and HC reagent lots was evaluated per time point on a NovaSeq 6000 sequencer, using three different sequencing reagent lots. The analysis of baseline timepoint zero (T0) identified the baseline variant calls for each sample. All five experimental time points have been processed and analyzed for Lot #1, Lot #2, and Lot #3. Concordance was assessed among 127,642 data points for tumor profiling variants across the five experimental timepoints. The three reagent lots achieved ≥90% concordance with the baseline variant calls for all the experimental timepoints (including the last two timepoints T4 and T5 at 12 and 13 months respectively) except for a middle timepoint T3 (9 months) which is present in Table 14. The reason for the failure of T3 (9 months) was due a technical error which resulted lower than planned DNA being transferred for LC and therefore was not a reagent failure. Reagent stability can be claimed as 12 months after the baseline testing date. **Table 14. Concordance for Tumor Profiling Variants at Replicate Level by Reagent Lot and by Timepoint** | Reagent Lot | Timepoint | # Concordant | # Total | Concordance (%) | 95% CI (%) | | --- | --- | --- | --- | --- | --- | | LOT#1 | 3 months | 1921 | 1966 | 97.71% | (96.95%, 98.28%) | | | 6 months | 2082 | 2151 | 96.79% | (95.96%, 97.46%) | | | 9 months | 1916 | 2151 | 89.07% | (87.69%, 90.32%) | | | 12 months | 1609 | 1656 | 97.16% | (96.25%, 97.86%) | | | 13 months | 1918 | 1973 | 97.21% | (96.39%, 97.85%) | | LOT#2 | 3 months | 2083 | 2148 | 96.97% | (96.16%, 97.62%) | | | 6 months | 2091 | 2160 | 96.81% | (95.98%, 97.47%) | | | 9 months | 1851 | 2160 | 85.69% | (84.15%, 87.11%) | | | 12 months | 2087 | 2160 | 96.62% | (95.77%, 97.3%) | | | 13 months | 2089 | 2160 | 96.71% | (95.87%, 97.39%) | | LOT#3 | 3 months | 2086 | 2139 | 97.52% | (96.77%, 98.10%) | | | 6 months | 2098 | 2154 | 97.4% | (96.64%, 97.99%) | | | 9 months | 1855 | 2154 | 86.12% | (84.59%, 87.51%) | | | 12 months | 2097 | 2154 | 97.35% | (96.59%, 97.95%) | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 22 of 46 {22} | Reagent Lot | Timepoint | # Concordant | # Total | Concordance (%) | 95% CI (%) | | --- | --- | --- | --- | --- | --- | | | 13 months | 1924 | 1977 | 97.32% | (96.51%, 97.94%) | b. Stability of cfDNA and Plasma Samples: See Summary of Safety and Effectiveness Data for P190032. c. Whole Blood Specimen Stability and Inverted Tube Stability: See Summary of Safety and Effectiveness Data for P190032 and Section XIII. ### 7. Guard-banding and Robustness: a. DNA Extraction: See Summary of Safety and Effectiveness Data for P190032. b. cfDNA Input: See Summary of Safety and Effectiveness Data for P190032 and P200006 and Section XIII. c. Molecular Index Barcode Performance: See Summary of Safety and Effectiveness Data for P190032. d. Automation Line Equivalence: See Summary of Safety and Effectiveness Data for P190032. ### B. Animal Studies Not Applicable ### C. Additional Studies #### 1. Blood Collection Tube Equivalence: See Summary of Safety and Effectiveness Data for P190032. ### X. SUMMARY OF PRIMARY CLINICAL STUDY The applicant performed a clinical bridging study to establish a reasonable assurance of safety and effectiveness of F1LCDx for the detection of SNVs and indels that lead to MET exon 14 skipping in the plasma of patients with NSCLC who may benefit from TABRECTA (capmatinib). Pre-treatment plasma samples and clinical outcome data from patients with NSCLC enrolled in the clinical study GEOMETRY mono-1 were used to establish a reasonable assurance of safety and effectiveness of F1LCDx for the indication for use of this PMA supplement. A summary of the clinical study is presented below. #### A. F1LCDx Clinical Bridging Study for SNVs and indels that lead to MET exon 14 skipping PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 23 of 46 {23} ## GEOMETRY mono-1 Study Design The GEOMETRY mono-1 study is a prospectively designed, multicenter, open-label, single arm Phase II study to evaluate the safety and efficacy of the MET inhibitor TABRECTA (capmatinib) in adult patients with EGFR wild-type (wt) and ALK-rearrangement negative, locally advanced or metastatic NSCLC harboring MET exon 14 skipping alterations. The primary objective was to assess overall response rate (ORR) by a Blinded Independent Review Committee (BIRC) assessment per Response Evaluation Criteria in Solid Tumors (RECIST) 1.1 criteria by cohort to determine whether treatment with TABRECTA is effective. Duration of response (DOR) as assessed by BIRC is the key secondary endpoint. GEOMETRY mono-1 is an ongoing study that was initiated on June 11, 2015 with first patient first visit. - Cohort 4 only enrolled pretreated (second and third line) patients with MET exon 14 deletions, and - Cohort 5b only enrolled treatment-naïve patients with MET exon 14 deletions. Patients were screened for enrollment into Cohorts 4 and 5b for MET exon 14 deletion status using tissue based MET exon 14 deletion reverse-transcriptase PCR (RT-PCR) clinical trial assay (CTA). Plasma samples were collected and stored prior to study treatment for retrospective testing. Patients enrolled in Cohorts 4 and 5b received 400mg of TABRECTA orally twice daily in tablet form. Efficacy was evaluated every six weeks from the first day of treatment until RECIST 1.1 disease progression. Plasma samples from other cohorts from GEOMETRY mono-1, cohorts 1b, 2 and 3 (MET exon 14 deletion negative) were included in the bridging study to supplement the analysis to calculate NPA for the sensitivity analysis. ## Clinical Bridging Study A clinical bridging study was conducted to evaluate: 1) the concordance between MET single nucleotide variants (SNVs) and indels that lead to MET exon 14 skipping status by the CTA and F1LCDx, and 2) the clinical validity of F1LCDx in identifying NSCLC patients with MET exon 14 skipping mutations who may be eligible for treatment with TABRECTA. Plasma samples from GEOMETRY mono-1 patients were collected by the therapeutic investigational sites per the study protocol and study documents and shipped to the central testing laboratories. Blood samples were collected on Cycle 1 Day 1 prior to treatment with the study drug for patients enrolled into the GEOMETRY mono-1 study, including MET exon 14 deletion positive patients in cohorts 4 and 5b, and MET exon 14 deletions negative patients in cohorts 1b, 2, and 3. In addition to MET mutation negative plasma samples were also collected from the GEOMETRY mono-1 trial, additional tissue-matched NSCLC samples from commercial sources were used to supplement this population. Plasma samples were shipped to Foundation Medicine for retrospective testing with F1LCDx assay. PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 24 of 46 {24} # 1. Clinical Inclusion and Exclusion Criteria The sample inclusion and exclusion criteria for the the retrospective testing of the clinical bridging study were: Sample inclusion criteria: - Samples from enrolled patients from Cohorts 1b, 2, 3, 4, and 5b with informed consent provided in the GEOMETRY mono-1 trial - Samples from commercial sources with informed consent confirmed under purchase contract - Samples from Cohorts 1b, 2, and 3 must have a valid CTA negative result from tissue - Frozen plasma specimens with a minimum plasma volume of 2.5mL - Samples were required to meet minimum criteria for F1LCDx assay operational testing requirements Sample exclusion criteria: - Lack of clear subject identification or label on stored patient sample - Obvious physical damage of stored patient sample - Tissue and other liquid samples - Samples with plasma volume <2.5mL Specimens included in the clinical bridging study were tested according to the standard testing protocol for the F1LCDx assay test with a minimum recommended cfDNA input of ≥ 30 ng for the library construction step. A subset of patient specimens were also tested at lower cfDNA inputs of ≥ 20 ng and <30 ng cfDNA input based on pre-specified assay procedures and processed only if the samples passed pre-specified in-process quality criteria. : In the instances where a sample had ≥20 and <30ng following DNA extraction, the sample was tested. This reflects FMI's current practice of processing samples with <30 ng cfDNA for input into the assay in cases where the clinician is contacted and there is not sufficient sample to be re-run. # 2. Follow up Schedule The F1LCDx clinical bridging study involved retrospective testing of plasma samples; as such, no additional patient follow-up was conducted. # 3. Clinical Endpoints The primary endpoint of GEOMETRY mono-1 is the overall response rate (ORR) by Blinded Independent Review Committee (BIRC) assessment by cohort to determine whether treatment with capmatinib is effective. Duration of response (DOR) as assessed by BIRC is the key secondary endpoint. # B. Accountability of PMA Cohort As of clinical study data cut-off of April 15, 2019, 223 patients were enrolled into Cohorts 1b, 2, 3, 4, and 5b of GEOMETRY mono-1 and included for the device clinical bridging study. Of these 223 patients, 97 were enrolled into Cohorts 4 and 5b based on PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 25 of 46 {25} MET exon 14 skipping status determined using FFPE tissue by the CTA. Of the 97 CTA-enrolled patients, 69 were enrolled in Cohort 4 (2nd and 3rd line, pre-treated) and 28 were enrolled in Cohort 5b (1st line, treatment-naïve). Ninety-three (93) of the 97 CTA enrolled patients had available plasma and were included for the retrospective F1LCDx testing. Among them, 81 samples met the F1LCDx recommended sample input of cfDNA ≥ 30 ng, while 7 additional samples met the minimum F1LCDx sample input criteria of cfDNA ≥ 20 ng. Five (5) patient samples did not yield sufficient cfDNA of ≥ 20 ng and were not tested by F1LCDx. The remaining 126 out of 223 patients have also been tested for MET exon 14 skipping status by the CTA, either prospectively or retrospectively. These are NSCLC patients with various levels of MET amplification enrolled into Cohorts 1b, 2, or 3 of GEOMETRY mono-1 study. Of the 126 patients, 88 were CTA(-) for MET exon 14 skipping and had plasma samples available to be included in retrospective F1LCDx testing. Twenty-one (21) CTA(-) samples from NSCLC patients from commercial source with plasma volume ≥ 2.5 mL were also included for F1LCDx testing. As described above, a total of 202 samples, including 93 from Cohorts 4 and 5b, 88 from Cohorts 1b, 2, and 3, and 21 from commercial sources were sent to FMI for processing. Once accessioned by FMI, cfDNA was subsequently extracted and samples were tested only when cfDNA available for test input was ≥ 20 ng. A total of 185 of the 202 samples mentioned above have met these criteria after extraction at FMI. One hundred sixty-six (166) samples from GEOMETRY mono-1 and 19 commercial samples were confirmed to have pooled plasma volumes ≥ 2.5 mL and yielded the minimum F1LCDx input required of cfDNA (≥20 ng). Samples tested with ≥ 30 ng and ≥ 20 ng cfDNA input were included in both the primary concordance analyses and the primary clinical efficacy analyses. Of the 185 samples tested by F1LCDx, 150 were tested with ≥ 30 ng of cfDNA and reported valid results. An additional 21 samples were tested with ≥ 20 ng and < 30 ng cfDNA with valid results. This makes up a total of 171 samples with valid F1LCDx results for statistical analysis. Among the 202 samples sent to FMI, 31 were excluded from the statistical analysis due to not being evaluated or producing invalid results. Within them, 17 had cfDNA yields below the 20 ng minimum required test input and were therefore not tested by F1LCDx. The other 14 were excluded due to failed quality metrics during F1LCDx testing and reported as invalid. The detailed sample accountability is available in Figure 1. Figure 1: GEOMETRY mono-1 sample accountability in combined cohorts PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 26 of 46 {26}  The statistical analysis was performed on all CTA(+) subjects from Cohort 4 and 5b, CTA(-) subjects from Cohort 1b, Cohort 2 and Cohort 3 of GEOMETRY mono-1, as well as all available plasma samples from commercial sources meeting minimum requirements of 2.5mL plasma and CTA(-) tissue-matched NSCLC. All the CTA(-) enrolled subjects were randomly assigned to Cohort 4 and Cohort 5b with the probabilities proportional to the samples size of each cohort in order to conduct cohort-based statistical analyses. The CTA(-) tissue-matched commercial samples were assigned to Cohort 4 and Cohort 5b based on pre-treatment status. Any samples with unknown pre-treatment status were randomly assigned to Cohort 4 and Cohort 5b with the probabilities proportional to the sample size of each cohort. The primary analysis set for Cohort 4 (PAS-A) in the bridging study included all these CTA(+) subjects from the Cohort 4 of original GEOMETRY mono-1 trial who have one or two prior lines of systemic therapy. It also included the CTA(-) subjects assigned to this population as described above. The PAS-A was evaluated for the concordance analysis and the efficacy analysis. The primary analysis set for Cohort 5b (PAS-B) in the bridging study included all these CTA(+) subjects from the Cohort 5b of original GEOMETRY mono-1 trial who must be treatment naive for advanced disease. It also included the CTA- negative subjects assigned to this population as described above. The PAS-B was evaluated for the concordance analysis and the efficacy analysis. Overall, the primary concordance analysis of F1LCDx with the CTA was performed using the combined sample numbers from PAS-A and PAS-B from the GEOMETRY mono-1 trial and commercial sources. A total of 150 patients (136 from GEOMETRY mono-1 and 14 from commercial source) with valid CTA results were tested with F1LCDx at ≥ 30 ng cfDNA input and yielded valid F1LCDx results. The concordance PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 27 of 46 {27} analysis was also performed on the 171 patients (153 from GEOMETRY mono-1 and 18 from commercial source) with valid CTA results that were tested with F1LCDx at ≥ 20 ng cfDNA input and yielded valid F1LCDx results. Full disposition of the patient samples from GEOMETRY mono-1 and those used for the F1LCDx bridging study is shown in Tables 15 and 16. Table 15: Disposition of all GEOMETRY mono-1 bridging subjects | | Total patients | Samples sent to FMI for CDx(1) | Actual Tested by CDx(2) | | --- | --- | --- | --- | | Total enrolled in Cohort 1b, 2, 3, 4 and 5b (as of 04/15/19 data cut-off) | 223 | 181 | 166 | | Tested as CTA-positive (enrolled only in C4 and C5b) | 97 | 93 | 88 | | Enrolled in Cohort 4 | 69 | 66 | 61 | | Enrolled in Cohort 5b | 28 | 27 | 27 | | Tested as CTA-negative (enrolled only in C1b, C2 and C3) | 126 | 88 | 78 | | Randomized to cohort 4 for bridging analysis | 63 | 63 | 57 | | Randomized to cohort 5b for bridging analysis | 25 | 25 | 21 | | Total commercial CTA-negative | 21 | 21 | 19 | | Assigned to cohort 4 for bridging analysis | 2 | 2 | 2 | | Assigned to cohort 5b for bridging analysis | 19 | 19 | 17 | | Total samples included | 244 | 202 | 185 | | Samples not sent to FMI | 42 | 0 | 0 | | Samples sent to FMI for CDx testing but not tested by CDx | 17 | 17 | 0 | | Samples tested as invalid by CDx | 14 | 14 | 14 | (1)Samples with estimated volume ≥ 2.5 mL (2)Samples with cfDNA input level ≥ 20 ng Table 16: Disposition of GEOMETRY mono-1 bridging subjects for CDx and CTA (PAS-A/PAS-B) | CDx | CTA | | | --- | --- | --- | | | Positive N=97 (%) | Negative N=109 (%) | | Tested with cfDNA input ≥30 ng | | | | Positive | 55 (56.7) | 0 | | Negative | 23 (23.7) | 72 (66.1) | | Invalid | 3 (3.1) | 6 (5.5) | | Tested with cfDNA input ≥20 ng | | | | Positive | 57 (58.8) | 0 | | Negative | 26 (26.8) | 88 (80.7) | | Invalid | 5 (5.2) | 9 (8.3) | | Not tested | 9 (9.3) | 12 (11.0) | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 28 of 46 {28} The analysis of clinical utility based on ORR was performed in only GEOMETRY mono-1 patients who have been assigned into Cohorts 4 and 5b, respectively, according to the statistical analysis plan. The clinical utility results presented here include only the F1LCDx MET exon 14 skipping mutation positive population of 39 patients from Cohort 4 and 16 patients from Cohort 5b with valid F1LCDx results, tested with cfDNA ≥ 30 ng. Efficacy analysis on ORR was also performed for the F1LCDx MET exon 14 skipping mutation positive population of 41 patients from Cohort 4 and 16 patients from Cohort 5b with valid F1LCDx results, tested with cfDNA ≥ 20 ng. Sensitivity analyses were conducted on the concordance and efficacy results to determine the impact of missing F1LCDx results patients. It included those not tested, invalid result under the ≥30 ng and ≥20 ng cfDNA input, and those tested with cfDNA ≥ 20 ng and < 30 ng under the recommended input. The sensitivity analysis demonstrated that the clinical efficacy analyses are robust to missing F1LCDx results. ### C. Study Population Demographics and Baseline Parameters The demographics, disease characteristics and specimen characteristics for the F1LCDx evaluable and F1LCDx-unevaluable patients were similar for all of the CTA- enrolled patients in both the GEOMETRY mono-1 MET exon 14 skipping positive Cohorts 4 and 5b (Tables 17 and 18). Table 17: Comparison of demographic and disease characteristics between F1LCDx-evaluable and F1LCDx-unevaluable set for CTA(+) patients in Cohort 4 by F1LCDx sample requirements (PAS-A) F1LCDx sample requirement: Recommended (cfDNA input ≥ 30 ng) | Baseline characteristics | CDx evaluable N=53 | CDx unevaluable N=16 | All N=69 | | --- | --- | --- | --- | | Age (years) | | | | | n | 53 | 16 | 69 | | Mean | 70.7 | 71.9 | 71.0 | | SD | 7.93 | 9.74 | 8.32 | | Median | 71.0 | 70.0 | 71.0 | | Minimum | 54.0 | 49.0 | 49.0 | | Maximum | 88.0 | 90.0 | 90.0 | | Sex-n (%) | | | | | Female | 32 (60.4) | 8 (50.0) | 40 (58.0) | | Male | 21 (39.6) | 8 (50.0) | 29 (42.0) | | Race-n (%) | | | | | Caucasian | 38 (71.7) | 11 (68.8) | 49 (71.0) | | Asian | 14 (26.4) | 5 (31.3) | 19 (27.5) | | Native American | 1 (1.9) | 0 | 1 (1.4) | | ECOG at baseline-n (%) | | | | | 0 | 13 (24.5) | 3 (18.8) | 16 (23.2) | | 1 | 39 (73.6) | 13 (81.3) | 52 (75.4) | | 2 | 1 (1.9) | 0 | 1 (1.4) | | Histological grade-n (%) | | | | | Well Differentiated | 3 (5.7) | 2 (12.5) | 5 (7.2) | | Moderately Differentiated | 6 (11.3) | 3 (18.8) | 9 (13.0) | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 29 of 46 {29} | Baseline characteristics | CDx evaluable N=53 | CDx unevaluable N=16 | All N=69 | | --- | --- | --- | --- | | Poorly Differentiated | 15 (28.3) | 4 (25.0) | 19 (27.5) | | Undifferentiated | 4 (7.5) | 1 (6.3) | 5 (7.2) | | Unknown | 25 (47.2) | 6 (37.5) | 31 (44.9) | | Stage at study entry-n (%) | | | | | Stage IIIB | 1 (1.9) | 1 (6.3) | 2 (2.9) | | Stage IV | 52 (98.1) | 15 (93.8) | 67 (97.1) | - All % calculated using N as denominator - SD = Standard Deviation F1LCDx sample requirement: Minimum (cfDNA input ≥ 20 ng) | Baseline characteristics | CDx evaluable N=57 | CDx unevaluable N=12 | All N=69 | | --- | --- | --- | --- | | Age (years) | | | | | n | 57 | 12 | 69 | | Mean | 70.9 | 71.5 | 71.0 | | SD | 7.73 | 11.14 | 8.32 | | Median | 71.0 | 68.0 | 71.0 | | Minimum | 54.0 | 49.0 | 49.0 | | Maximum | 88.0 | 90.0 | 90.0 | | Sex-n (%) | | | | | Female | 33 (57.9) | 7 (58.3) | 40 (58.0) | | Male | 24 (42.1) | 5 (41.7) | 29 (42.0) | | Race-n (%) | | | | | Caucasian | 39 (68.4) | 10 (83.3) | 49 (71.0) | | Asian | 17 (29.8) | 2 (16.7) | 19 (27.5) | | Native American | 1 (1.8) | 0 | 1 (1.4) | | ECOG at baseline-n (%) | | | | | 0 | 14 (24.6) | 2 (16.7) | 16 (23.2) | | 1 | 42 (73.7) | 10 (83.3) | 52 (75.4) | | 2 | 1 (1.8) | 0 | 1 (1.4) | | Histological grade-n (%) | | | | | Well Differentiated | 3 (5.3) | 2 (16.7) | 5 (7.2) | | Moderately Differentiated | 7 (12.3) | 2 (16.7) | 9 (13.0) | | Poorly Differentiated | 17 (29.8) | 2 (16.7) | 19 (27.5) | | Undifferentiated | 4 (7.0) | 1 (8.3) | 5 (7.2) | | Unknown | 26 (45.6) | 5 (41.7) | 31 (44.9) | | Stage at study entry-n (%) | | | | | Stage IIIB | 1 (1.8) | 1 (8.3) | 2 (2.9) | | Stage IV | 56 (98.2) | 11 (91.7) | 67 (97.1) | - All % calculated using N as denominator - SD = Standard Deviation Table 18: Comparison of demographic and disease characteristics between CDx-evaluable and CDx-unevaluable set for CTA-positive patients in Cohort 5b by CDx sample requirements (PAS-B) F1LCDx sample requirement: Recommended (cfDNA input ≥ 30 ng) | Baseline characteristics | CDx evaluable N=25 | CDx unevaluable N=3 | All N=28 | | --- | --- | --- | --- | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 30 of 46 {30} | Age (years) | | | | | --- | --- | --- | --- | | n | 25 | 3 | 28 | | Mean | 72.5 | 71.7 | 72.4 | | SD | 6.58 | 12.01 | 7.02 | | Median | 71.0 | 71.0 | 71.0 | | Minimum | 57.0 | 60.0 | 57.0 | | Maximum | 86.0 | 84.0 | 86.0 | | Sex-n (%) | | | | | Female | 15 (60.0) | 3 (100) | 18 (64.3) | | Male | 10 (40.0) | 0 | 10 (35.7) | | Race-n (%) | | | | | Caucasian | 21 (84.0) | 3 (100) | 24 (85.7) | | Asian | 4 (16.0) | 0 | 4 (14.3) | | ECOG at baseline-n (%) | | | | | 0 | 7 (28.0) | 0 | 7 (25.0) | | 1 | 18 (72.0) | 3 (100) | 21 (75.0) | | Histological grade-n (%) | | | | | Well Differentiated | 4 (16.0) | 0 | 4 (14.3) | | Moderately Differentiated | 0 | 2 (66.7) | 2 (7.1) | | Poorly Differentiated | 6 (24.0) | 0 | 6 (21.4) | | Undifferentiated | 2 (8.0) | 0 | 2 (7.1) | | Unknown | 13 (52.0) | 1 (33.3) | 14 (50.0) | | Stage at study entry-n (%) | | | | | Stage IV | 25 (100) | 3 (100) | 28 (100) | - All % calculated using N as denominator - SD = Standard Deviation F1LCDx sample requirement: Minimum (cfDNA input ≥ 20 ng) | Baseline characteristics | CDx evaluable N=26 | CDx unevaluable N=2 | All N=28 | | --- | --- | --- | --- | | Age (years) | | | | | n | 26 | 2 | 28 | | Mean | 72.5 | 72.0 | 72.4 | | SD | 6.45 | 16.97 | 7.02 | | Median | 71.0 | 72.0 | 71.0 | | Minimum | 57.0 | 60.0 | 57.0 | | Maximum | 86.0 | 84.0 | 86.0 | | Sex-n (%) | | | | | Female | 16 (61.5) | 2 (100) | 18 (64.3) | | Male | 10 (38.5) | 0 | 10 (35.7) | | Race-n (%) | | | | | Caucasian | 22 (84.6) | 2 (100) | 24 (85.7) | | Asian | 4 (15.4) | 0 | 4 (14.3) | | ECOG at baseline-n (%) | | | | | 0 | 7 (26.9) | 0 | 7 (25.0) | | 1 | 19 (73.1) | 2 (100) | 21 (75.0) | | Histological grade-n (%) | | | | | Well Differentiated | 4 (15.4) | 0 | 4 (14.3) | | Moderately Differentiated | 1 (3.8) | 1 (50.0) | 2 (7.1) | | Poorly Differentiated | 6 (23.1) | 0 | 6 (21.4) | PMA P190032/S001: FDA Summary of Safety and Effectiveness Data 31 of 46 {31} | Baseline characteristics | CDx evaluable N=26 | CDx unevaluable N=2 | All N=28 | | --- | --- | --- | --- | | Undifferentiated | 2 (7.7) | 0 | 2 (7.1) | | Unknown | 13 (50.0) | 1 (50.0) | 14 (50.0) | | Stage at study entry-n (%) | | | | | Stage IV | 26 (100) | 2 (100) | 28 (100) | - All % calculated using N as denominator - SD = Standard Deviation ### D. Safety and Effectiveness Results #### 1. Safety Results The safety with respect to treatment with TABRECTA was addressed during the review of the NDA and is not addressed in detail in this Summary of Safety and Effectiveness Data. The evaluation of safety was based on the analysis of adverse events (AEs), clinical laboratory evaluations, physical examinations, and vital signs. Please refer to Drugs@FDA for complete safety i…