Accurate de novo and transmitted indel detection in exome-capture data using microassembly

Narzisi, G., O'Rawe, Jason, Iossifov, I., Fang, Han, Lee, Y. H., Wang, Zihua, Wu, Yiyang, Lyon, Gholson J., Wigler, M. H., Schatz, M. C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nature Methods, 11 (10). pp. 1033-1036.

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URL: http://www.ncbi.nlm.nih.gov/pubmed/25128977
DOI: 10.1038/nmeth.3069

Abstract

We present an open-source algorithm, Scalpel (http://scalpel.sourceforge.net/), which combines mapping and assembly for sensitive and specific discovery of insertions and deletions (indels) in exome-capture data. A detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for indel discovery, particularly in regions containing near-perfect repeats. We analyzed 593 families from the Simons Simplex Collection and demonstrated Scalpel's power to detect long (≥30 bp) transmitted events and enrichment for de novo likely gene-disrupting indels in autistic children.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > insertion/deletion
Investigative techniques and equipment > whole exome sequencing
Investigative techniques and equipment > assays > whole exome sequencing
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics
CSHL labs > Iossifov lab
CSHL labs > Lyon lab
CSHL labs > Schatz lab
CSHL labs > Wigler lab
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: Andrea Potopsingh
Date Deposited: 02 Sep 2014 13:41
Last Modified: 04 Nov 2015 21:25
PMCID: PMC4180789
Related URLs:
URI: http://repository.cshl.edu/id/eprint/30720

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