The Molecular/Genomic Diagnostics Gym

Question 1

Commonly used metrics and quality control parameters used to assess run performance for NGS wet bench process documentation include:

A. Percentage of reads mapping to the target region
B. Fraction of bases meeting specified quality and coverage thresholds
C. Average coverage per base

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Answer 1

All of the above.

See Aziz et al. (College of American Pathologists’ Laboratory Standards for Next-Generation Sequencing Clinical Tests APLM 2014)

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Question 2

Essential performance characteristics that need to be determined during internal validation include:

A. Analytic sensitivity
B. Analytic specificity
C. Accuracy
D. Precision
E. Limit of detection

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Answer 2

All of the above.

See Aziz et al. (College of American Pathologists’ Laboratory Standards for Next-Generation Sequencing Clinical Tests APLM 2014)

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Question 3

According to the framework proposed by the ACCE, genetic tests should be evaluated on which of the following criteria:

A. Analytical validity
B. Clinical validity
C. Clinical utility
D. Ethical, legal and social issues

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Answer 3

All of the above.

See Easton et al. (NEJM 2015)

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Question 4

In vitro diagnostics that have gone through and passed a 510(k) trial are considered FDA-approved - True/False

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Answer 4

False. FDA-cleared.

See Halling et al. (APLM 2012)

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Question 5

"Verification" and "validation" pertain to FDA-approved/cleared and laboratory-developed tests respectively - True/False

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Answer 5

True.

See Halling et al. (APLM 2012)

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Question 6

The mnemonic PARR+AS+AS is most relevant to FDA-approved/cleared tests - True/False

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Answer 6

False. LDT.

PARR for FDA-approved/cleared tests.

See Halling et al. (APLM 2012)

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Question 7

Professional organizations or state agencies demonstrating that their accreditation requirements meet or exceed those specified by CLIA have "deemed status" from CMS (Centers for Medicare 7 Medicaid Services) to accredit laboratories - True/False

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Answer 7

True.

See Jennings et al. (APLM 2009)

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Question 8

When applied to qualitative tests, "accuracy" is equivalent to "sensitivity and specificity" - True/False

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Answer 8

True.

See Jennings et al. (APLM 2009)

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Question 9

True/False: Although the terms depth and coverage can be used interchangeably, coverage has also been used to denote the breadth of coverage of a target genome.

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Answer 9

True.

See Sims et al. (Sequencing depth and coverage: key considerations in genomic analyses, 2014)