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.

Characterization of Missing Human Genome Sequences and Copy-number Polymorphic Insertions / J. Kidd, N. Sampas, F. Antonacci, T. Graves, R. Fulton, H. Hayden, C. Alkan, M. Malig, M. Ventura, G. Giannuzzi, J. Kallicki, P. Anderson, A. Tsalenko, N. Yamada, P. Tsang, R. Kaul, R. Wilson, L. Bruhn, E. Eichler. - In: NATURE METHODS. - ISSN 1548-7091. - 7:5(2010), pp. 365-371. [10.1038/NMETH.1451]

Characterization of Missing Human Genome Sequences and Copy-number Polymorphic Insertions

G. Giannuzzi;
2010

Abstract

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.
Settore BIO/18 - Genetica
Article (author)
File in questo prodotto:
File Dimensione Formato  
nmeth.1451.pdf

accesso aperto

Tipologia: Publisher's version/PDF
Dimensione 1.18 MB
Formato Adobe PDF
1.18 MB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

Caricamento pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/863062
Citazioni
  • ???jsp.display-item.citation.pmc??? 73
  • Scopus 109
  • ???jsp.display-item.citation.isi??? 101
social impact