Mapping segmental and sequence variations among laboratory mice using BAC array CGH

Antoine M. Snijders; Norma J. Nowak; Bing Huey; Jane Fridlyand; Sindy Law; Jeffrey Conroy; Taku Tokuyasu; Kubilay Demir; Readman Chiu; Jian Hua Mao; Ajay N. Jain; Steven J.M. Jones; Allan Balmain; Daniel Pinkel; Donna G. Albertson

doi:10.1101/gr.2902505

Mapping segmental and sequence variations among laboratory mice using BAC array CGH

Antoine M. Snijders
, Norma J. Nowak
, Bing Huey
, Jane Fridlyand
, Sindy Law
, Jeffrey Conroy
, Taku Tokuyasu
, Kubilay Demir
, Readman Chiu
, Jian Hua Mao
, Ajay N. Jain
, Steven J.M. Jones
, Allan Balmain
, Daniel Pinkel
, Donna G. Albertson

Biochemistry

University of California at San Francisco
Roswell Park Cancer Institute
Genome Sequence Centre

Research output: Contribution to journal › Article › peer-review

61 Scopus citations

Abstract

We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation ( log₂ratio ≥ 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Δ log₂ratio ∼0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

Original language	English
Pages (from-to)	302-311
Number of pages	10
Journal	Genome Research
Volume	15
Issue number	2
DOIs	https://doi.org/10.1101/gr.2902505
State	Published - 2005

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@article{6a8128b9d66b4f958d4e2ad0b4febce6,

title = "Mapping segmental and sequence variations among laboratory mice using BAC array CGH",

abstract = "We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation ( log2ratio ≥ 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Δ log2ratio ∼0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.",

author = "Snijders, \{Antoine M.\} and Nowak, \{Norma J.\} and Bing Huey and Jane Fridlyand and Sindy Law and Jeffrey Conroy and Taku Tokuyasu and Kubilay Demir and Readman Chiu and Mao, \{Jian Hua\} and Jain, \{Ajay N.\} and Jones, \{Steven J.M.\} and Allan Balmain and Daniel Pinkel and Albertson, \{Donna G.\}",

year = "2005",

doi = "10.1101/gr.2902505",

language = "English",

volume = "15",

pages = "302--311",

journal = "Genome Research",

issn = "1088-9051",

publisher = "Cold Spring Harbor Laboratory Press",

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TY - JOUR

T1 - Mapping segmental and sequence variations among laboratory mice using BAC array CGH

AU - Snijders, Antoine M.

AU - Nowak, Norma J.

AU - Huey, Bing

AU - Fridlyand, Jane

AU - Law, Sindy

AU - Conroy, Jeffrey

AU - Tokuyasu, Taku

AU - Demir, Kubilay

AU - Chiu, Readman

AU - Mao, Jian Hua

AU - Jain, Ajay N.

AU - Jones, Steven J.M.

AU - Balmain, Allan

AU - Pinkel, Daniel

AU - Albertson, Donna G.

PY - 2005

Y1 - 2005

N2 - We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation ( log2ratio ≥ 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Δ log2ratio ∼0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

AB - We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation ( log2ratio ≥ 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Δ log2ratio ∼0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

UR - https://www.scopus.com/pages/publications/20044371978

U2 - 10.1101/gr.2902505

DO - 10.1101/gr.2902505

M3 - Article

C2 - 15687294

AN - SCOPUS:20044371978

SN - 1088-9051

VL - 15

SP - 302

EP - 311

JO - Genome Research

JF - Genome Research

IS - 2

ER -

Mapping segmental and sequence variations among laboratory mice using BAC array CGH

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