schliessen

Filtern

 

Bibliotheken

Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one

Deep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC–peptide tetramers, cannot... Full description

Journal Title: Immunogenetics 2014, Vol.66(1), pp.15-24
Main Author: Dudley, Dawn
Other Authors: Karl, Julie , Creager, Hannah , Bohn, Patrick , Wiseman, Roger , O’Connor, David
Format: Electronic Article Electronic Article
Language: English
Subjects:
ID: ISSN: 0093-7711 ; E-ISSN: 1432-1211 ; DOI: 10.1007/s00251-013-0744-3
Link: http://dx.doi.org/10.1007/s00251-013-0744-3
Zum Text:
SendSend as email Add to Book BagAdd to Book Bag
Staff View
recordid: springer_jour10.1007/s00251-013-0744-3
title: Full-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one
format: Article
creator:
  • Dudley, Dawn
  • Karl, Julie
  • Creager, Hannah
  • Bohn, Patrick
  • Wiseman, Roger
  • O’Connor, David
subjects:
  • Major histocompatibility complex class I
  • Chinese rhesus macaques
  • Roche/454 pyrosequencing
  • Illumina MiSeq sequencing
  • MHC class I genotyping
ispartof: Immunogenetics, 2014, Vol.66(1), pp.15-24
description: Deep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC–peptide tetramers, cannot be directly obtained by short read deep sequencing. We combined data from two next-generation sequencing platforms to discover novel full-length MHC class I mRNA/cDNA transcripts in Chinese rhesus macaques. We first genotyped macaques by Roche/454 pyrosequencing using a 530-bp amplicon spanning the densely polymorphic exons 2 through 4 of the MHC class I loci that encode the peptide-binding region. We then mapped short paired-end 250 bp Illumina sequence reads spanning the full-length transcript to each 530-bp amplicon at high stringency and used paired-end information to reconstruct full-length allele sequences. We characterized 65 full-length sequences from six Chinese rhesus macaques. Overall, approximately 70 % of the alleles distinguished in these six animals contained new sequence information, including 29 novel transcripts. The flexibility of this approach should make full-length MHC class I allele genotyping accessible for any nonhuman primate population of interest. We are currently optimizing this method for full-length characterization of other highly polymorphic, duplicated loci such as the MHC class II DRB and killer immunoglobulin-like receptors. We anticipate that this method will facilitate rapid expansion and near completion of sequence libraries of polymorphic loci, such as MHC class I, within a few years.
language: eng
source:
identifier: ISSN: 0093-7711 ; E-ISSN: 1432-1211 ; DOI: 10.1007/s00251-013-0744-3
fulltext: fulltext
issn:
  • 1432-1211
  • 14321211
  • 0093-7711
  • 00937711
url: Link


@attributes
ID1120133998
RANK0.07
NO1
SEARCH_ENGINEprimo_central_multiple_fe
SEARCH_ENGINE_TYPEPrimo Central Search Engine
LOCALfalse
PrimoNMBib
record
control
sourcerecordid10.1007/s00251-013-0744-3
sourceidspringer_jour
recordidTN_springer_jour10.1007/s00251-013-0744-3
sourcesystemOther
pqid1492626778
galeid354367734
display
typearticle
titleFull-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one
creatorDudley, Dawn ; Karl, Julie ; Creager, Hannah ; Bohn, Patrick ; Wiseman, Roger ; O’Connor, David
ispartofImmunogenetics, 2014, Vol.66(1), pp.15-24
identifier
subjectMajor histocompatibility complex class I ; Chinese rhesus macaques ; Roche/454 pyrosequencing ; Illumina MiSeq sequencing ; MHC class I genotyping
descriptionDeep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC–peptide tetramers, cannot be directly obtained by short read deep sequencing. We combined data from two next-generation sequencing platforms to discover novel full-length MHC class I mRNA/cDNA transcripts in Chinese rhesus macaques. We first genotyped macaques by Roche/454 pyrosequencing using a 530-bp amplicon spanning the densely polymorphic exons 2 through 4 of the MHC class I loci that encode the peptide-binding region. We then mapped short paired-end 250 bp Illumina sequence reads spanning the full-length transcript to each 530-bp amplicon at high stringency and used paired-end information to reconstruct full-length allele sequences. We characterized 65 full-length sequences from six Chinese rhesus macaques. Overall, approximately 70 % of the alleles distinguished in these six animals contained new sequence information, including 29 novel transcripts. The flexibility of this approach should make full-length MHC class I allele genotyping accessible for any nonhuman primate population of interest. We are currently optimizing this method for full-length characterization of other highly polymorphic, duplicated loci such as the MHC class II DRB and killer immunoglobulin-like receptors. We anticipate that this method will facilitate rapid expansion and near completion of sequence libraries of polymorphic loci, such as MHC class I, within a few years.
languageeng
source
version8
lds50peer_reviewed
links
openurl$$Topenurl_article
openurlfulltext$$Topenurlfull_article
backlink$$Uhttp://dx.doi.org/10.1007/s00251-013-0744-3$$EView_full_text_in_Springer_(Subscribers_only)
search
creatorcontrib
0Dudley, Dawn, M.
1Karl, Julie, A.
2Creager, Hannah, M.
3Bohn, Patrick, S.
4Wiseman, Roger, W.
5O’Connor, David, H.
titleFull-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one
descriptionDeep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC–peptide tetramers, cannot be directly obtained by short read deep sequencing. We combined data from two next-generation sequencing platforms to discover novel full-length MHC class I mRNA/cDNA transcripts in Chinese rhesus macaques. We first genotyped macaques by Roche/454 pyrosequencing using a 530-bp amplicon spanning the densely polymorphic exons 2 through 4 of the MHC class I loci that encode the peptide-binding region. We then mapped short paired-end 250 bp Illumina sequence reads spanning the full-length transcript to each 530-bp amplicon at high stringency and used paired-end information to reconstruct full-length allele sequences. We characterized 65 full-length sequences from six Chinese rhesus macaques. Overall, approximately 70 % of the alleles distinguished in these six animals contained new sequence information, including 29 novel transcripts. The flexibility of this approach should make full-length MHC class I allele genotyping accessible for any nonhuman primate population of interest. We are currently optimizing this method for full-length characterization of other highly polymorphic, duplicated loci such as the MHC class II DRB and killer immunoglobulin-like receptors. We anticipate that this method will facilitate rapid expansion and near completion of sequence libraries of polymorphic loci, such as MHC class I, within a few years.
subject
0Major histocompatibility complex class I
1Chinese rhesus macaques
2Roche/454 pyrosequencing
3Illumina MiSeq sequencing
4MHC class I genotyping
general
010.1007/s00251-013-0744-3
1English
2Springer Science & Business Media B.V.
3SpringerLink
sourceidspringer_jour
recordidspringer_jour10.1007/s00251-013-0744-3
issn
01432-1211
114321211
20093-7711
300937711
rsrctypearticle
creationdate2014
addtitleImmunogenetics
searchscopespringer_journals_complete
scopespringer_journals_complete
lsr30VSR-Enriched:[pages, pqid, galeid]
sort
titleFull-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one
authorDudley, Dawn ; Karl, Julie ; Creager, Hannah ; Bohn, Patrick ; Wiseman, Roger ; O’Connor, David
creationdate20140100
facets
frbrgroupid3392307331853700284
frbrtype5
languageeng
creationdate2014
topic
0Major Histocompatibility Complex Class I
1Chinese Rhesus Macaques
2Roche/454 Pyrosequencing
3Illumina Miseq Sequencing
4Mhc Class I Genotyping
collectionSpringerLink
prefilterarticles
rsrctypearticles
creatorcontrib
0Dudley, Dawn
1Karl, Julie
2Creager, Hannah
3Bohn, Patrick
4Wiseman, Roger
5O’Connor, David
jtitleImmunogenetics
toplevelpeer_reviewed
delivery
delcategoryRemote Search Resource
fulltextfulltext
addata
aulast
0Dudley
1Karl
2Creager
3Bohn
4Wiseman
5O’Connor
aufirst
0Dawn
1M.
2Julie
3A.
4Hannah
5Patrick
6S.
7Roger
8W.
9David
10H.
au
0Dudley, Dawn
1Karl, Julie
2Creager, Hannah
3Bohn, Patrick
4Wiseman, Roger
5O’Connor, David
atitleFull-length novel MHC class I allele discovery by next-generation sequencing: two platforms are better than one
jtitleImmunogenetics
stitleImmunogenetics
risdate201401
volume66
issue1
spage15
epage24
issn0093-7711
eissn1432-1211
genrearticle
ristypeJOUR
abstractDeep sequencing has revolutionized major histocompatibility complex (MHC) class I analysis of nonhuman primates by enabling high-throughput, economical, and comprehensive genotyping. Full-length MHC class I cDNA sequences, which are required to generate reagents such as MHC–peptide tetramers, cannot be directly obtained by short read deep sequencing. We combined data from two next-generation sequencing platforms to discover novel full-length MHC class I mRNA/cDNA transcripts in Chinese rhesus macaques. We first genotyped macaques by Roche/454 pyrosequencing using a 530-bp amplicon spanning the densely polymorphic exons 2 through 4 of the MHC class I loci that encode the peptide-binding region. We then mapped short paired-end 250 bp Illumina sequence reads spanning the full-length transcript to each 530-bp amplicon at high stringency and used paired-end information to reconstruct full-length allele sequences. We characterized 65 full-length sequences from six Chinese rhesus macaques. Overall, approximately 70 % of the alleles distinguished in these six animals contained new sequence information, including 29 novel transcripts. The flexibility of this approach should make full-length MHC class I allele genotyping accessible for any nonhuman primate population of interest. We are currently optimizing this method for full-length characterization of other highly polymorphic, duplicated loci such as the MHC class II DRB and killer immunoglobulin-like receptors. We anticipate that this method will facilitate rapid expansion and near completion of sequence libraries of polymorphic loci, such as MHC class I, within a few years.
copBerlin/Heidelberg
pubSpringer Berlin Heidelberg
doi10.1007/s00251-013-0744-3
pages15-24
date2014-01