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

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

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Narzisi, Giuseppe O'Rawe, Jason A. Iossifov, Ivan Fang, Han Lee, Yoon-Ha Wang, Zihua Wu, Yiyang Lyon, Gholson J. Wigler, Michael Schatz, Michael C.
Description	Country affiliation: United States Author Affiliation: Narzisi G ( 1] Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] New York Genome Center, New York, USA.); O'Rawe JA ( 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.); Iossifov I ( Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.); Fang H ( 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.); Lee YH ( Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.); Wang Z ( Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.); Wu Y ( 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.); Lyon GJ ( 1] Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Stony Brook University, Stony Brook, New York, USA.); Wigler M ( Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.); Schatz MC ( Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.)
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.
File Format	HTM / HTML
ISSN	15487091
e-ISSN	15487105
DOI	10.1038/nmeth.3069
Journal	Nature Methods
Issue Number	10
Volume Number	11
Language	English
Publisher	Nature Publishing Group
Publisher Date	2014-10-01
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Discipline Clinical Laboratory Techniques Dna Mutational Analysis Exome Indel Mutation Algorithms Computational Biology Chemistry Databases, Genetic Mutation Programming Languages Sequence Alignment Research Support, N.i.h., Extramural Research Support, Non-u.s. Gov't Research Support, U.s. Gov't, Non-p.h.s.
Content Type	Text
Resource Type	Article
Subject	Cell Biology Biochemistry Molecular Biology Biotechnology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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