#39 · Genomics
New callers resolve CNVs, structural variants, uniparental disomy and aneuploidy from NGS
The items share a methodological thread: detecting genomic copy-number, structural and chromosome-level alterations from short- and long-read sequencing. gSV combines alignment- and assembly-based evidence through maximum exact matches to call structural variants from third-generation data. ML-ExonCNV pairs XGBoost with a multi-expert ensemble to detect rare exon-level CNVs in whole-exome data, reporting outperformance against GATK-gCNV and ExomeDepth. PScnv applies panel-of-normals ridge normalization with hierarchical multi-phase calling for targeted panels. UPDhmm uses a hidden Markov model to detect uniparental disomy from trio data, and a separate study detects autosomal and sex chromosome aneuploidies, including mosaics, from clinical and exome NGS data. What is new is the extension of these callers across sequencing modalities and across event classes, including mosaicism and uniparental disomy, rather than a single regulatory question.
Published papers
ML-ExonCNV: a robust XGBoost multi-expert ensemble framework for rare exon CNV detection in whole-exome sequencing data.
ML-ExonCNV pairs XGBoost with a multi-expert ensemble to detect rare exon-level CNVs from whole-exome sequencing, outperforming GATK-gCNV, ExomeDepth and…
UPDhmm: detecting uniparental disomy from NGS trio data.
UPDhmm, an HMM-based R/Bioconductor tool, detects uniparental disomy from trio exome/genome data, outperforming existing methods on simulations and finding…
PScnv: personalized self-normalizing CNV detection with a hierarchical multi-phase framework.
PScnv is a personalized self-normalizing CNV caller for targeted panel sequencing, combining panel-of-normals ridge normalization with hierarchical multi-phase…
Identification of autosomal and sex chromosome aneuploidies using next generation sequencing.
Detects autosomal and sex chromosome aneuploidies, including mosaics, from clinical and whole exome NGS data; scripts released.
Preprints
gSV: a general structural variant detector using the third-generation sequencing data
gSV is a general structural variant caller for long-read data that combines alignment- and assembly-based evidence via maximum exact matches, improving complex…
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