Limits...
A high-resolution map of segmental DNA copy number variation in the mouse genome.

Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ - PLoS Genet. (2006)

Bottom Line: In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation.We demonstrate that this technique can identify copy number differences associated with known polymorphic traits.The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St. Louis, Missouri, United States of America. graubert@medicine.wustl.edu

ABSTRACT
Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.

Show MeSH

Related in: MedlinePlus

Representative Germline CNVs in Mice Identified by High-Resolution aCGHThe log2 ratios of signal intensity for C57BL/6J (reference) versus 20 test strains are shown. Inset, an expanded view of the CNVs in NOD/LtJ and A/J from (A) and (B). Scale, 500 kb.(A) A 135.6-kb segment of reduced copy number (mean log2 = −1.02) on Chromosome 14 is present in most strains.(B) A 61.7-kb amplified segment (mean log2 = +1.01) on Chromosome 1 is present in most strains.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1761046&req=5

pgen-0030003-g001: Representative Germline CNVs in Mice Identified by High-Resolution aCGHThe log2 ratios of signal intensity for C57BL/6J (reference) versus 20 test strains are shown. Inset, an expanded view of the CNVs in NOD/LtJ and A/J from (A) and (B). Scale, 500 kb.(A) A 135.6-kb segment of reduced copy number (mean log2 = −1.02) on Chromosome 14 is present in most strains.(B) A 61.7-kb amplified segment (mean log2 = +1.01) on Chromosome 1 is present in most strains.

Mentions: We performed comparative genomic hybridization using long oligonucleotide arrays (oligo-aCGH) containing 388,352 probes spanning the mouse reference genome with a median spacing of 5 kb. Germline DNA from 20 high-priority MPD strains was tested against the C57BL/6J reference strain. Segmental germline DNA copy number gains and losses were evident in all strains (Figure 1). By using a set of stringent criteria (see Materials and Methods), 80 “high confidence” CNVs were identified. CNVs were detected on all 19 mouse autosomes (Figure 2). Changes on the X and Y chromosomes were not considered in this analysis because of lower probe density and greater mapping uncertainty for these regions in the current assembly. The segments vary in size (range, 21.4 kb to 2.0 Mb; mean, 271.5 kb) and number per strain (range, two CNVs per genome in C57BL/6Tac to 38 CNVs per genome in NOD/LtJ; mean, 22 CNVs per genome) (Table S1). As expected, no segments were identified in the C57BL/6J self–self hybridization. While the tiling-path design used in this study enables systematic detection of CNVs in genic and intergenic regions, we note that repeat-masking yields a subset of regions (e.g., the centromeres) with lower probe density, which could affect the CNV detection rate. Despite the lower probe coverage in these regions, several high confidence CNVs were detected in areas of relatively low probe coverage (Figure S1).


A high-resolution map of segmental DNA copy number variation in the mouse genome.

Graubert TA, Cahan P, Edwin D, Selzer RR, Richmond TA, Eis PS, Shannon WD, Li X, McLeod HL, Cheverud JM, Ley TJ - PLoS Genet. (2006)

Representative Germline CNVs in Mice Identified by High-Resolution aCGHThe log2 ratios of signal intensity for C57BL/6J (reference) versus 20 test strains are shown. Inset, an expanded view of the CNVs in NOD/LtJ and A/J from (A) and (B). Scale, 500 kb.(A) A 135.6-kb segment of reduced copy number (mean log2 = −1.02) on Chromosome 14 is present in most strains.(B) A 61.7-kb amplified segment (mean log2 = +1.01) on Chromosome 1 is present in most strains.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1761046&req=5

pgen-0030003-g001: Representative Germline CNVs in Mice Identified by High-Resolution aCGHThe log2 ratios of signal intensity for C57BL/6J (reference) versus 20 test strains are shown. Inset, an expanded view of the CNVs in NOD/LtJ and A/J from (A) and (B). Scale, 500 kb.(A) A 135.6-kb segment of reduced copy number (mean log2 = −1.02) on Chromosome 14 is present in most strains.(B) A 61.7-kb amplified segment (mean log2 = +1.01) on Chromosome 1 is present in most strains.
Mentions: We performed comparative genomic hybridization using long oligonucleotide arrays (oligo-aCGH) containing 388,352 probes spanning the mouse reference genome with a median spacing of 5 kb. Germline DNA from 20 high-priority MPD strains was tested against the C57BL/6J reference strain. Segmental germline DNA copy number gains and losses were evident in all strains (Figure 1). By using a set of stringent criteria (see Materials and Methods), 80 “high confidence” CNVs were identified. CNVs were detected on all 19 mouse autosomes (Figure 2). Changes on the X and Y chromosomes were not considered in this analysis because of lower probe density and greater mapping uncertainty for these regions in the current assembly. The segments vary in size (range, 21.4 kb to 2.0 Mb; mean, 271.5 kb) and number per strain (range, two CNVs per genome in C57BL/6Tac to 38 CNVs per genome in NOD/LtJ; mean, 22 CNVs per genome) (Table S1). As expected, no segments were identified in the C57BL/6J self–self hybridization. While the tiling-path design used in this study enables systematic detection of CNVs in genic and intergenic regions, we note that repeat-masking yields a subset of regions (e.g., the centromeres) with lower probe density, which could affect the CNV detection rate. Despite the lower probe coverage in these regions, several high confidence CNVs were detected in areas of relatively low probe coverage (Figure S1).

Bottom Line: In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation.We demonstrate that this technique can identify copy number differences associated with known polymorphic traits.The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci.

View Article: PubMed Central - PubMed

Affiliation: Department of Medicine, Division of Oncology, Stem Cell Biology Section, Washington University, St. Louis, Missouri, United States of America. graubert@medicine.wustl.edu

ABSTRACT
Submicroscopic (less than 2 Mb) segmental DNA copy number changes are a recently recognized source of genetic variability between individuals. The biological consequences of copy number variants (CNVs) are largely undefined. In some cases, CNVs that cause gene dosage effects have been implicated in phenotypic variation. CNVs have been detected in diverse species, including mice and humans. Published studies in mice have been limited by resolution and strain selection. We chose to study 21 well-characterized inbred mouse strains that are the focus of an international effort to measure, catalog, and disseminate phenotype data. We performed comparative genomic hybridization using long oligomer arrays to characterize CNVs in these strains. This technique increased the resolution of CNV detection by more than an order of magnitude over previous methodologies. The CNVs range in size from 21 to 2,002 kb. Clustering strains by CNV profile recapitulates aspects of the known ancestry of these strains. Most of the CNVs (77.5%) contain annotated genes, and many (47.5%) colocalize with previously mapped segmental duplications in the mouse genome. We demonstrate that this technique can identify copy number differences associated with known polymorphic traits. The phenotype of previously uncharacterized strains can be predicted based on their copy number at these loci. Annotation of CNVs in the mouse genome combined with sequence-based analysis provides an important resource that will help define the genetic basis of complex traits.

Show MeSH
Related in: MedlinePlus