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REPLACED BY V5 on AUGUST 31, 2022
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Analytical Validity, Clinical Validation summary worksheet, NGS in Inherited Cancer Testing (NGS-PF-006-v4)
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Instructions: Please complete the following tables and answer the following questions as appropriate. Indicate "N/A" when not applicable.
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NOTE: There are 10 Sections in this form.
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1 - DEX Z-CodeTM Identifier:
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2 - List indications for use (list the cancer type(s) indicated for use of this test, add rows if necessary):
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A:
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3a- Is this test utilizing an FDA-approved or cleared kit?
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A:Yes/No:
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If yes, please provide the vendor and kit name:
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3b-Is this test utilizing a non FDA-approved commercial kit?
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A:Yes/No:
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If yes, please provide the vendor and kit name:
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4 - Preanalytical Questions
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1. What are the sample types accepted for testing?
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2. Is a trio or comparator required for analysis?
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3. Describe orthogonal methods used for confirmation of the clinical validation:
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5 - Analytical Questions
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1. Describe the library quality criteria for reporting:
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2. Describe variant quality criteria for reporting:
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3. What is the mean depth of coverage across validation samples:
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4. What is your minimum accepted mean depth of coverage for a clinical sample:
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5. Describe non-NGS methodologies used to cover complex regions:
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6 - Post-Analytical
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1. Who reviews and signs out these test results?
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2. How are controls utilized in this test?
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3. How do you ensure specimen integrity/ minimize contamination?
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4. How do you handle negative or QNS reports?
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5. How do you handle amended and corrected reports?
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7 - Sample Types Tested in Clinical Validation
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List the samples (or controls) used for the validation and number used. Add rows to describe "Other" sample types, if necessary.
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Sample Type
Number of Samples Tested
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Whole Blood
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Saliva
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Saliva Swab
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Buccal Swab
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Cultured Cells
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Tissue
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Extracted DNA
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Other
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*Reference Material
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Total clinical samples in validation
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Total samples in validation
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*Reference material are not considered "clinical" and do not contribute to the assessment of the clinical validation.
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8 - Analytical validation summary table
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Column12345678
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Variant Type1Variant allele frequency rangeUnique SamplesUnique Variants Expected3Unique variants detectedConcordant Unique VariantsSensitivity/ Variant-level PPA (95% CI)Specificity/ Variant-level NPA (95% CI)Variant-level Reproducibility
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SNVs
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Indels ≤40bp
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Indels >40bp
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CNVs (Gain/Loss)
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SVs
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SSVs2
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Repeat Expansion
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Other (fill in variant type)
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1Types = Single Nucleotide variant (SNV), Insertion/Deletion (INDELs), Copy Number Variant (CNV), Structural Variant (SV), Splice-Site Variant (SSV)
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2 For the purposes of this table, a splice-site variant is defined as a variant that is detected by analyzing RNA transcripts.
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3 For the purposes of this table, a “unique variant” may include the same variant [e.g., BRCA1 c.4327C>T (p.Arg1443Ter)] in different unique samples.
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9 - Required Genes
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Complete the table below, add more lines if necessary
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NOTE: genes are ONLY required for tests where the cancer type listed is included in the intended use of the test.
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GeneTranscriptMalignancy indicationIs the gene covered by this assay (Y/N)?Are all exons covered by this assay? (Y/N)Exons not coveredExons covered by alternate methodologyComment
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APCColon
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ATMBreast, Prostate
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BMPR1AColon
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BRCA1Breast, Ovarian, Pancreatic, Prostate
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BRCA2Breast, Ovarian, Pancreatic, Prostate
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BRIP1Ovarian
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CDH1Breast
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CDKN2APancreatic
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CHEK2Breast, Prostate
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EPCAMOvarian, Colon, Endometrial, Gastric
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MLH1Colon, Pancreatic, Prostate, Endometrial, Gastric
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MSH2Colon, Prostate, Endometrial, Gastric
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MSH6Colon, Prostate, Endometrial, Gastric
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MUTYHColon
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NBNBreast
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NF1Breast
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PALB2Breast, Pancreatic, Prostate
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PMS2Colon, Prostate
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PTENBreast, Colon
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RAD51COvarian
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RAD51DOvarian
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SMAD4Colorectal
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STK11Breast, Pancreatic, Colorectal
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TP53Breast, Pancreatic, Colorectal