A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization

Yuen-Jun Chung, Jos Jonkers, Hannah Kitson, Heike Fiegler, Sean Humphray, Carol Scott, Sarah Hunt, Yuejin Yu, Ichiko Nishijima, Arno Velds, Henne Holstege, Nigel Carter, Allan Bradley

Research output: Contribution to journalArticleAcademicpeer-review

Abstract

Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.
Original languageEnglish
Pages (from-to)188-196
JournalGenome Research
Volume14
Issue number1
DOIs
Publication statusPublished - 2004
Externally publishedYes

Cite this

Chung, Yuen-Jun ; Jonkers, Jos ; Kitson, Hannah ; Fiegler, Heike ; Humphray, Sean ; Scott, Carol ; Hunt, Sarah ; Yu, Yuejin ; Nishijima, Ichiko ; Velds, Arno ; Holstege, Henne ; Carter, Nigel ; Bradley, Allan. / A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. In: Genome Research. 2004 ; Vol. 14, No. 1. pp. 188-196.
@article{5f21ec0a5a26427ea6c9333ec355b9ad,
title = "A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization",
abstract = "Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.",
author = "Yuen-Jun Chung and Jos Jonkers and Hannah Kitson and Heike Fiegler and Sean Humphray and Carol Scott and Sarah Hunt and Yuejin Yu and Ichiko Nishijima and Arno Velds and Henne Holstege and Nigel Carter and Allan Bradley",
year = "2004",
doi = "10.1101/gr.1878804",
language = "English",
volume = "14",
pages = "188--196",
journal = "Genome Research",
issn = "1088-9051",
publisher = "Cold Spring Harbor Laboratory Press",
number = "1",

}

Chung, Y-J, Jonkers, J, Kitson, H, Fiegler, H, Humphray, S, Scott, C, Hunt, S, Yu, Y, Nishijima, I, Velds, A, Holstege, H, Carter, N & Bradley, A 2004, 'A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization' Genome Research, vol. 14, no. 1, pp. 188-196. https://doi.org/10.1101/gr.1878804

A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization. / Chung, Yuen-Jun; Jonkers, Jos; Kitson, Hannah; Fiegler, Heike; Humphray, Sean; Scott, Carol; Hunt, Sarah; Yu, Yuejin; Nishijima, Ichiko; Velds, Arno; Holstege, Henne; Carter, Nigel; Bradley, Allan.

In: Genome Research, Vol. 14, No. 1, 2004, p. 188-196.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - A whole-genome mouse BAC microarray with 1-Mb resolution for analysis of DNA copy number changes by array comparative genomic hybridization

AU - Chung, Yuen-Jun

AU - Jonkers, Jos

AU - Kitson, Hannah

AU - Fiegler, Heike

AU - Humphray, Sean

AU - Scott, Carol

AU - Hunt, Sarah

AU - Yu, Yuejin

AU - Nishijima, Ichiko

AU - Velds, Arno

AU - Holstege, Henne

AU - Carter, Nigel

AU - Bradley, Allan

PY - 2004

Y1 - 2004

N2 - Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.

AB - Microarray-based comparative genomic hybridization (CGH) has become a powerful method for the genome-wide detection of chromosomal imbalances. Although BAC microarrays have been used for mouse CGH studies, the resolving power of these analyses was limited because high-density whole-genome mouse BAC microarrays were not available. We therefore developed a mouse BAC microarray containing 2803 unique BAC clones from mouse genomic libraries at 1-Mb intervals. For the general amplification of BAC clone DNA prior to spotting, we designed a set of three novel degenerate oligonucleotide-primed (DOP) PCR primers that preferentially amplify mouse genomic sequences while minimizing unwanted amplification of contaminating Escherichia coli DNA. The resulting 3K mouse BAC microarrays reproducibly identified DNA copy number alterations in cell lines and primary tumors, such as single-copy deletions, regional amplifications, and aneuploidy.

UR - https://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=9144262347&origin=inward

UR - https://www.ncbi.nlm.nih.gov/pubmed/14707179

U2 - 10.1101/gr.1878804

DO - 10.1101/gr.1878804

M3 - Article

VL - 14

SP - 188

EP - 196

JO - Genome Research

JF - Genome Research

SN - 1088-9051

IS - 1

ER -