DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Genome Research

Volumn 24, Issue 12, 2014, Pages 2022-2032

  Scheinin, Ilari ^a,b   Sie, Daoud ^a   Bengtsson, Henrik ^c,d   Van De Wiel, Mark A ^a,e   Olshen, Adam B ^c,d   Van Thuijl, Hinke F ^a   Van Essen, Hendrik F ^a   Eijk, Paul P ^a   Rustenburg, Franҫois ^a   Meijer, Gerrit A ^a   Reijneveld, Jaap C ^a,f   Wesseling, Pieter ^a,g   Pinkel, Daniel ^c,d   Albertson, Donna G ^c,d,h   Ylstra, Bauke ^a  

^a VU UNIVERSITY MEDICAL CENTER   (Netherlands)

^b HELSINKI UNIVERSITY CENTRAL HOSPITAL   (Finland)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e VU UNIVERSITY AMSTERDAM   (Netherlands)

^f ACADEMIC MEDICAL CENTER   (Netherlands)

^g RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^h NEW YORK UNIVERSITY COLLEGE OF DENTISTRY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COST; DNA BASE COMPOSITION; FORMALIN FIXED PARAFFIN EMBEDDED SECTION; GENE DOSAGE; GENE SEQUENCE; GENOME; HUMAN; HUMAN TISSUE; MICROARRAY ANALYSIS; SIGNAL NOISE RATIO; TISSUE SECTION; WHOLE GENOME SEQUENCING; ALGORITHM; BIOLOGY; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER PROGRAM; COPY NUMBER VARIATION; GENETICS; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN GENOME; NEOPLASM; PROCEDURES; TUMOR CELL LINE;

ALGORITHMS; BASE COMPOSITION; CELL LINE, TUMOR; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTATIONAL BIOLOGY; DNA COPY NUMBER VARIATIONS; GENOME, HUMAN; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; NEOPLASMS; SOFTWARE;

EID: 84913590291     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.175141.114     Document Type: Article

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