Characterization of missing human genome sequences and copy-number polymorphic insertions.
The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 new insertion sequences corresponding to 720 genomic loci. We found that a substantial fraction of these sequences are either missing, fragmented or misassigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determined that 18-37% of these new insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identified new exons and conserved noncoding sequences not yet represented in the reference genome. We developed a method to accurately genotype these new insertions by mapping next-generation sequencing datasets to the breakpoint, thereby providing a means to characterize copy-number status for regions previously inaccessible to single-nucleotide polymorphism microarrays.
Kidd
Jeffrey M
JM
Department of Genome Sciences, University of Washington School of Medicine, Seattle, USA.
Sampas
Nick
N
Antonacci
Francesca
F
Graves
Tina
T
Fulton
Robert
R
Hayden
Hillary S
HS
Alkan
Can
C
Malig
Maika
M
Ventura
Mario
M
Giannuzzi
Giuliana
G
Kallicki
Joelle
J
Anderson
Paige
P
Tsalenko
Anya
A
Yamada
N Alice
NA
Tsang
Peter
P
Kaul
Rajinder
R
Wilson
Richard K
RK
Bruhn
Laurakay
L
Eichler
Evan E
EE
D020451:Contig Mapping / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics; D005787:Gene Frequency; D015894:Genome, Human; D056914:Genomic Structural Variation / Q000235:genetics; D005838:Genotype; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008969:Molecular Sequence Data; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA / Q000379:methods*
D004251:DNA Transposable Elements