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Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

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Updated: Jan 2, 2026

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

gDNA Enrichment by a Transposase-based Technology for NGS Analysis of the Whole Sequence of BRCA1, BRCA2, and 9 Genes Involved in DNA Damage Repair

Published on: October 6, 2014

An optimized BRCA1/2 next-generation sequencing for different clinical sample types.

Yoonjung Kim¹, Chi Heum Cho², Jung Sook Ha³

¹Department of Laboratory Medicine, Yonsei University College of Medicine, Seoul, Korea.

Journal of Gynecologic Oncology

|December 3, 2019

Summary

This summary is machine-generated.

For ovarian cancer patients, blood (buffy coat) is the superior sample type for germline BRCA1/2 mutation testing via next-generation sequencing (NGS). Tumor samples are better suited for detecting somatic mutations.

Keywords:

BRCA1 BRCA2 Blood Buffy Coat High-Throughput Nucleotide Sequencing Tissue Preservation

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Area of Science:

Oncology
Genetics
Molecular Biology

Background:

Simultaneous germline and somatic mutation detection in ovarian cancer (OC) using tumor tissue is cost-effective for BRCA1/2 testing.
Limited studies exist on the analytical performance of BRCA1/2 next-generation sequencing (NGS) across various sample types.

Purpose of the Study:

To propose a routine BRCA1/2 NGS screening strategy based on analytical performance across different sample types.
To evaluate the performance of BRCA1/2 NGS assays using buffy coat, fresh-frozen (FF), and formalin-fixed paraffin-embedded (FFPE) samples.

Main Methods:

Comparison of BRCA1/2 NGS screening assays.
Utilized 130 samples including buffy coat, FF, and FFPE.
Assessed analytical performances: accuracy, sensitivity, specificity, and positive predictive value (PPV).

Main Results:

Buffy coat showed 0% repeat tests, 100% accuracy, sensitivity, and specificity for BRCA1/2 NGS.
FFPE samples had a 34% repeat rate and 99.9% accuracy, but lower sensitivity (95.5%-99.0%) due to VAF shifts.
FFPE showed a 51.4% PPV, improved by ~20% post-filtration; FF had an 8% repeat rate.

Conclusions:

Buffy coat is unaffected by sequencing artifacts and VAF shifts, making it ideal for germline BRCA1/2 mutation detection.
Tumor materials (FFPE, FF) are suitable for detecting somatic mutations in OC patients when germline mutations are not the primary focus.