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Related Experiment Video

Updated: Jan 24, 2026

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

In Vivo Functional Study of Disease-associated Rare Human Variants Using Drosophila

Published on: August 20, 2019

Rare variant phasing using paired tumor:normal sequence data.

Alexandra R Buckley^1,2, Trey Ideker^3,4,5, Hannah Carter^3,4,5

¹Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.

BMC Bioinformatics

|May 29, 2019

Summary

This summary is machine-generated.

This study introduces Variant Allele Frequency (VAF) phasing, a new method for haplotype phasing using paired tumor:normal sequencing data. VAF phasing significantly increases the number of phased germline variants, aiding cancer predisposition gene research.

Keywords:

Cancer genomics Cancer germline Variant phasing

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Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Detection of Rare Mutations in CtDNA Using Next Generation Sequencing

Published on: August 24, 2017

Area of Science:

Genomics
Bioinformatics
Cancer Research

Background:

Haplotype phasing is crucial for understanding genetic variant-phenotype relationships.
Standard sequencing lacks chromosome origin assignment for genetic variants.
Phasing clarifies the impact of multiple variants within a single gene copy.

Purpose of the Study:

To present a novel haplotype phasing approach utilizing paired tumor:normal sequencing data.
To improve the accuracy and efficiency of genetic variant phasing in cancer studies.

Main Methods:

Developed Variant Allele Frequency (VAF) phasing method.
Applied VAF phasing to 6180 samples from The Cancer Genome Atlas (TCGA).
Compared VAF phasing concordance and variant yield against standard methods.

Main Results:

VAF phasing demonstrates high concordance with existing methods.
VAF phasing phases an average of 33% more variants than read-backed methods.
Suggestive association found between multiple missense variants in a gene copy and earlier cancer diagnosis.

Conclusions:

VAF phasing leverages tumor genome properties to enhance germline variant phasing.
The method surpasses standard read-backed approaches in paired tumor:normal samples.
Results highlight the need for tools assessing joint genetic variant effects.