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. (August 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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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:	Iossifov, Ivan Lee, Yoon-Ha Lyon, Gholson Narzisi, Giuseppe O'Rawe, Jason Schatz, Michael C. Wang, Zihua Wigler, Michael H. Wu, Yiyang
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:	17 August 2014
Date Deposited:	02 Sep 2014 13:41
Last Modified:	04 Nov 2015 21:25
PMCID:	PMC4180789
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/30720

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