PMID- 32355290
OWN - NLM
STAT- MEDLINE
DCOM- 20210106
LR  - 20210430
IS  - 2045-2322 (Electronic)
IS  - 2045-2322 (Linking)
VI  - 10
IP  - 1
DP  - 2020 Apr 30
TI  - Targeted analysis of polymorphic loci from low-coverage shotgun sequence data 
      allows accurate genotyping of HLA genes in historical human populations.
PG  - 7339
LID - 10.1038/s41598-020-64312-w [doi]
LID - 7339
AB  - The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in 
      adaptive immunity and is associated with various complex diseases. Accurate 
      analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding 
      their role in human adaptation to pathogens. Here, we describe the TARGT pipeline 
      for targeted analysis of polymorphic loci from low-coverage shotgun sequence 
      data. The pipeline was successfully applied to medieval aDNA samples and 
      validated using both simulated aDNA and modern empirical sequence data from the 
      1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA 
      polymorphisms in historical (and modern) human populations.
FAU - Pierini, Federica
AU  - Pierini F
AD  - Research Group for Evolutionary Immunogenomics, Max Planck Institute for 
      Evolutionary Biology, 24306, Ploen, Germany.
AD  - Universite Paris-Saclay, CNRS, Inria, Laboratoire de recherche en informatique, 
      91405, Orsay, France.
FAU - Nutsua, Marcel
AU  - Nutsua M
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Bohme, Lisa
AU  - Bohme L
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Ozer, Onur
AU  - Ozer O
AD  - Research Group for Evolutionary Immunogenomics, Max Planck Institute for 
      Evolutionary Biology, 24306, Ploen, Germany.
FAU - Bonczarowska, Joanna
AU  - Bonczarowska J
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Susat, Julian
AU  - Susat J
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Franke, Andre
AU  - Franke A
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Nebel, Almut
AU  - Nebel A
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Krause-Kyora, Ben
AU  - Krause-Kyora B
AD  - Institute of Clinical Molecular Biology, Kiel University, 24105, Kiel, Germany.
FAU - Lenz, Tobias L
AU  - Lenz TL
AD  - Research Group for Evolutionary Immunogenomics, Max Planck Institute for 
      Evolutionary Biology, 24306, Ploen, Germany. lenz@post.harvard.edu.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20200430
PL  - England
TA  - Sci Rep
JT  - Scientific reports
JID - 101563288
RN  - 0 (DNA, Ancient)
RN  - 0 (Genetic Markers)
RN  - 0 (HLA Antigens)
RN  - 0 (Histocompatibility Antigens Class II)
SB  - IM
MH  - Alleles
MH  - DNA, Ancient/*analysis
MH  - Denmark
MH  - Genetic Markers
MH  - Genetics, Population
MH  - Genome, Human
MH  - *Genotype
MH  - HLA Antigens/*genetics
MH  - Haplotypes
MH  - *High-Throughput Nucleotide Sequencing
MH  - Histocompatibility Antigens Class II/*genetics
MH  - Humans
MH  - Pattern Recognition, Automated
MH  - *Polymorphism, Single Nucleotide
PMC - PMC7193575
COIS- The authors declare no competing interests.
EDAT- 2020/05/02 06:00
MHDA- 2021/01/07 06:00
PMCR- 2020/04/30
CRDT- 2020/05/02 06:00
PHST- 2019/12/12 00:00 [received]
PHST- 2020/04/14 00:00 [accepted]
PHST- 2020/05/02 06:00 [entrez]
PHST- 2020/05/02 06:00 [pubmed]
PHST- 2021/01/07 06:00 [medline]
PHST- 2020/04/30 00:00 [pmc-release]
AID - 10.1038/s41598-020-64312-w [pii]
AID - 64312 [pii]
AID - 10.1038/s41598-020-64312-w [doi]
PST - epublish
SO  - Sci Rep. 2020 Apr 30;10(1):7339. doi: 10.1038/s41598-020-64312-w.