Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

Leslie A. Lyons; Thomas F. Laughlin; Neal G. Copeland; Nancy A. Jenkins; James E. Womack; Stephen J. O'Brien

doi:10.1038/ng0197-47

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

Leslie A. Lyons, Thomas F. Laughlin, Neal G. Copeland, Nancy A. Jenkins, James E. Womack, Stephen J. O'Brien

Research output: Contribution to journal › Review article › peer-review

333 Scopus citations

Abstract

Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.

Original language	English (US)
Pages (from-to)	47-56
Number of pages	10
Journal	Nature Genetics
Volume	15
Issue number	1
DOIs	https://doi.org/10.1038/ng0197-47
State	Published - Jan 1997

ASJC Scopus subject areas

Genetics

Access to Document

10.1038/ng0197-47

Cite this

@article{e631e15b9ef54f76a1c05ad2127c09ae,

title = "Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes",

abstract = "Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.",

author = "Lyons, {Leslie A.} and Laughlin, {Thomas F.} and Copeland, {Neal G.} and Jenkins, {Nancy A.} and Womack, {James E.} and O'Brien, {Stephen J.}",

year = "1997",

month = jan,

doi = "10.1038/ng0197-47",

language = "English (US)",

volume = "15",

pages = "47--56",

journal = "Nature Genetics",

issn = "1061-4036",

publisher = "Nature Publishing Group",

number = "1",

}

TY - JOUR

T1 - Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

AU - Lyons, Leslie A.

AU - Laughlin, Thomas F.

AU - Copeland, Neal G.

AU - Jenkins, Nancy A.

AU - Womack, James E.

AU - O'Brien, Stephen J.

PY - 1997/1

Y1 - 1997/1

N2 - Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.

AB - Precise comparisons of mammalian gene maps require common anchor loci as landmarks for conserved chromosomal segments. Using a computer script that automates DNA sequence database alignments, we designed 410 evolutionarily conserved primer pair sequences which are specific for anchor locus gene amplification from any mammalian species' DNA. Primer pairs were designed to span introns for polymorphism ascertainment, and to include sufficient exonic sequence (25-400 bp) to allow for gene identification. A total of 318 primer pairs were optimized for domestic cats, and 86% of the sequenced feline PCR products showed homology to the gene of primer origin. A screen of 20 mammals from 11 orders revealed that 35-52% of the 318 primers yielded a single PCR product without further optimization suggesting that nearly 75% can be optimized for any eutherian mammal.

UR - http://www.scopus.com/inward/record.url?scp=0031012314&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031012314&partnerID=8YFLogxK

U2 - 10.1038/ng0197-47

DO - 10.1038/ng0197-47

M3 - Review article

C2 - 8988168

AN - SCOPUS:0031012314

SN - 1061-4036

VL - 15

SP - 47

EP - 56

JO - Nature Genetics

JF - Nature Genetics

IS - 1

ER -

Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this