PMID- 28945251
OWN - NLM
STAT- MEDLINE
DCOM- 20171102
LR  - 20181113
IS  - 1546-1718 (Electronic)
IS  - 1061-4036 (Linking)
VI  - 49
IP  - 11
DP  - 2017 Nov
TI  - Graphtyper enables population-scale genotyping using pangenome graphs.
PG  - 1654-1660
LID - 10.1038/ng.3964 [doi]
AB  - A fundamental requirement for genetic studies is an accurate determination of 
      sequence variation. While human genome sequence diversity is increasingly well 
      characterized, there is a need for efficient ways to use this knowledge in 
      sequence analysis. Here we present Graphtyper, a publicly available novel 
      algorithm and software for discovering and genotyping sequence variants. 
      Graphtyper realigns short-read sequence data to a pangenome, a variation-aware 
      graph structure that encodes sequence variation within a population by 
      representing possible haplotypes as graph paths. Our results show that Graphtyper 
      is fast, highly scalable, and provides sensitive and accurate genotype calls. 
      Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 
      28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping 
      of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable 
      tool in characterizing sequence variation in both small and population-scale 
      sequencing studies.
FAU - Eggertsson, Hannes P
AU  - Eggertsson HP
AUID- ORCID: 0000-0002-1674-9978
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 
      Iceland.
FAU - Jonsson, Hakon
AU  - Jonsson H
AUID- ORCID: 0000-0001-6197-494X
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Kristmundsdottir, Snaedis
AU  - Kristmundsdottir S
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
FAU - Hjartarson, Eirikur
AU  - Hjartarson E
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Kehr, Birte
AU  - Kehr B
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - Berlin Institute of Health (BIH), Berlin, Germany.
FAU - Masson, Gisli
AU  - Masson G
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Zink, Florian
AU  - Zink F
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Hjorleifsson, Kristjan E
AU  - Hjorleifsson KE
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Jonasdottir, Aslaug
AU  - Jonasdottir A
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Jonasdottir, Adalbjorg
AU  - Jonasdottir A
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
FAU - Jonsdottir, Ingileif
AU  - Jonsdottir I
AUID- ORCID: 0000-0001-8339-150X
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 
      Iceland.
FAU - Gudbjartsson, Daniel F
AU  - Gudbjartsson DF
AUID- ORCID: 0000-0002-5222-9857
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 
      Iceland.
FAU - Melsted, Pall
AU  - Melsted P
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - School of Engineering and Natural Sciences, University of Iceland, Reykjavik, 
      Iceland.
FAU - Stefansson, Kari
AU  - Stefansson K
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, 
      Iceland.
FAU - Halldorsson, Bjarni V
AU  - Halldorsson BV
AUID- ORCID: 0000-0003-0756-0767
AD  - deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
AD  - School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.
LA  - eng
PT  - Journal Article
DEP - 20170925
PL  - United States
TA  - Nat Genet
JT  - Nature genetics
JID - 9216904
RN  - 0 (HLA Antigens)
SB  - IM
MH  - *Algorithms
MH  - Alleles
MH  - Base Sequence
MH  - Computer Graphics
MH  - *Genome, Human
MH  - Genotyping Techniques/*instrumentation
MH  - HLA Antigens/genetics
MH  - Haplotypes
MH  - High-Throughput Nucleotide Sequencing
MH  - Humans
MH  - *Polymorphism, Single Nucleotide
MH  - Sequence Alignment
MH  - Sequence Analysis, DNA/methods/*statistics & numerical data
MH  - Software
EDAT- 2017/09/26 06:00
MHDA- 2017/11/03 06:00
CRDT- 2017/09/26 06:00
PHST- 2017/06/20 00:00 [received]
PHST- 2017/09/01 00:00 [accepted]
PHST- 2017/09/26 06:00 [pubmed]
PHST- 2017/11/03 06:00 [medline]
PHST- 2017/09/26 06:00 [entrez]
AID - ng.3964 [pii]
AID - 10.1038/ng.3964 [doi]
PST - ppublish
SO  - Nat Genet. 2017 Nov;49(11):1654-1660. doi: 10.1038/ng.3964. Epub 2017 Sep 25.