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Correlating Multiallelic Copy Number Polymorphisms with Disease Susceptibility

Cantsilieris, Stuart ; White, Stefan J.

Hindawi Limited ; 2013

In: Human Mutation Vol. 34, No. 1 ( 2013-01), p. 1-13

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In: Human Mutation, Hindawi Limited, Vol. 34, No. 1 ( 2013-01), p. 1-13

Type of Medium: Online Resource

ISSN: 1059-7794

URL: Article

DOI: 10.1002/humu.22172

Language: English

Publisher: Hindawi Limited

Publication Date: 2013

detail.hit.zdb_id: 1498165-8

SSG: 12

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Rare variants in non-coding regulatory regions of the genome that affect gene expression in systemic lupus erythematosus

Jones, Sarah A. ; Cantsilieris, Stuart ; Fan, Huapeng ; [et al.]

Springer Science and Business Media LLC ; 2019

In: Scientific Reports Vol. 9, No. 1 ( 2019-10-28)

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In: Scientific Reports, Springer Science and Business Media LLC, Vol. 9, No. 1 ( 2019-10-28)

Abstract: Personalized medicine approaches are increasingly sought for diseases with a heritable component. Systemic lupus erythematosus (SLE) is the prototypic autoimmune disease resulting from loss of immunologic tolerance, but the genetic basis of SLE remains incompletely understood. Genome wide association studies (GWAS) identify regions associated with disease, based on common single nucleotide polymorphisms (SNPs) within them, but these SNPs may simply be markers in linkage disequilibrium with other, causative mutations. Here we use an hierarchical screening approach for prediction and testing of true functional variants within regions identified in GWAS; this involved bioinformatic identification of putative regulatory elements within close proximity to SLE SNPs, screening those regions for potentially causative mutations by high resolution melt analysis, and functional validation using reporter assays. Using this approach, we screened 15 SLE associated loci in 143 SLE patients, identifying 7 new variants including 5 SNPs and 2 insertions. Reporter assays revealed that the 5 SNPs were functional, altering enhancer activity. One novel variant was linked to the relatively well characterized rs9888739 SNP at the ITGAM locus, and may explain some of the SLE heritability at this site. Our study demonstrates that non-coding regulatory elements can contain private sequence variants affecting gene expression, which may explain part of the heritability of SLE.

Type of Medium: Online Resource

ISSN: 2045-2322

URL: Article

DOI: 10.1038/s41598-019-51864-9

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2019

detail.hit.zdb_id: 2615211-3

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Recurrent inversion toggling and great ape genome evolution

Porubsky, David ; Sanders, Ashley D. ; Höps, Wolfram ; [et al.]

Springer Science and Business Media LLC ; 2020

In: Nature Genetics Vol. 52, No. 8 ( 2020-08), p. 849-858

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 52, No. 8 ( 2020-08), p. 849-858

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/s41588-020-0646-x

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2020

detail.hit.zdb_id: 1494946-5

SSG: 12

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Identification of a rare coding variant in complement 3 associated with age-related macular degeneration

Zhan, Xiaowei ; Larson, David E ; Wang, Chaolong ; [et al.]

Springer Science and Business Media LLC ; 2013

In: Nature Genetics Vol. 45, No. 11 ( 2013-11), p. 1375-1379

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In: Nature Genetics, Springer Science and Business Media LLC, Vol. 45, No. 11 ( 2013-11), p. 1375-1379

Type of Medium: Online Resource

ISSN: 1061-4036 , 1546-1718

URL: Article

DOI: 10.1038/ng.2758

RVK:

XA 10000

Language: English

Publisher: Springer Science and Business Media LLC

Publication Date: 2013

detail.hit.zdb_id: 1494946-5

SSG: 12

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Recurrent structural variation, clustered sites of selection, and disease risk for the complement factor H ( CFH ) gene family

Cantsilieris, Stuart ; Nelson, Bradley J. ; Huddleston, John ; [et al.]

Proceedings of the National Academy of Sciences ; 2018

In: Proceedings of the National Academy of Sciences Vol. 115, No. 19 ( 2018-05-08)

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In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 115, No. 19 ( 2018-05-08)

Abstract: Structural variation and single-nucleotide variation of the complement factor H ( CFH ) gene family underlie several complex genetic diseases, including age-related macular degeneration (AMD) and atypical hemolytic uremic syndrome (AHUS). To understand its diversity and evolution, we performed high-quality sequencing of this ∼360-kbp locus in six primate lineages, including multiple human haplotypes. Comparative sequence analyses reveal two distinct periods of gene duplication leading to the emergence of four CFH -related ( CFHR ) gene paralogs ( CFHR2 and CFHR4 ∼25–35 Mya and CFHR1 and CFHR3 ∼7–13 Mya). Remarkably, all evolutionary breakpoints share a common ∼4.8-kbp segment corresponding to an ancestral CFHR gene promoter that has expanded independently throughout primate evolution. This segment is recurrently reused and juxtaposed with a donor duplication containing exons 8 and 9 from ancestral CFH , creating four CFHR fusion genes that include lineage-specific members of the gene family. Combined analysis of 〉 5,000 AMD cases and controls identifies a significant burden of a rare missense mutation that clusters at the N terminus of CFH [ P = 5.81 × 10 −8 , odds ratio (OR) = 9.8 (3.67-Infinity)]. A bipolar clustering pattern of rare nonsynonymous mutations in patients with AMD ( P 〈 10 −3 ) and AHUS ( P = 0.0079) maps to functional domains that show evidence of positive selection during primate evolution. Our structural variation analysis in 〉 2,400 individuals reveals five recurrent rearrangement breakpoints that show variable frequency among AMD cases and controls. These data suggest a dynamic and recurrent pattern of mutation critical to the emergence of new CFHR genes but also in the predisposition to complex human genetic disease phenotypes.

Type of Medium: Online Resource

ISSN: 0027-8424 , 1091-6490

URL: Article

DOI: 10.1073/pnas.1717600115

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: Proceedings of the National Academy of Sciences

Publication Date: 2018

detail.hit.zdb_id: 209104-5

detail.hit.zdb_id: 1461794-8

SSG: 11

SSG: 12

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Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region

Mohajeri, Kiana ; Cantsilieris, Stuart ; Huddleston, John ; [et al.]

Cold Spring Harbor Laboratory ; 2016

In: Genome Research Vol. 26, No. 11 ( 2016-11), p. 1453-1467

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In: Genome Research, Cold Spring Harbor Laboratory, Vol. 26, No. 11 ( 2016-11), p. 1453-1467

Abstract: Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion ( P = 7.8 × 10 −5 ). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.

Type of Medium: Online Resource

ISSN: 1088-9051 , 1549-5469

URL: Article

DOI: 10.1101/gr.211284.116

RVK:

XA 10000

Language: English

Publisher: Cold Spring Harbor Laboratory

Publication Date: 2016

detail.hit.zdb_id: 1483456-X

SSG: 12

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Adaptive archaic introgression of copy number variants and the discovery of previously unknown human genes

Hsieh, PingHsun ; Vollger, Mitchell R. ; Dang, Vy ; [et al.]

American Association for the Advancement of Science (AAAS) ; 2019

In: Science Vol. 366, No. 6463 ( 2019-10-18)

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In: Science, American Association for the Advancement of Science (AAAS), Vol. 366, No. 6463 ( 2019-10-18)

Abstract: Copy number variants (CNVs) are subject to stronger selective pressure than single-nucleotide variants, but their roles in archaic introgression and adaptation have not been systematically investigated. We show that stratified CNVs are significantly associated with signatures of positive selection in Melanesians and provide evidence for adaptive introgression of large CNVs at chromosomes 16p11.2 and 8p21.3 from Denisovans and Neanderthals, respectively. Using long-read sequence data, we reconstruct the structure and complex evolutionary history of these polymorphisms and show that both encode positively selected genes absent from most human populations. Our results collectively suggest that large CNVs originating in archaic hominins and introgressed into modern humans have played an important role in local population adaptation and represent an insufficiently studied source of large-scale genetic variation.

Type of Medium: Online Resource

ISSN: 0036-8075 , 1095-9203

URL: Article

DOI: 10.1126/science.aax2083

RVK:

TA 1000

RVK:

WA 15000

Language: English

Publisher: American Association for the Advancement of Science (AAAS)

Publication Date: 2019

detail.hit.zdb_id: 128410-1

detail.hit.zdb_id: 2066996-3

detail.hit.zdb_id: 2060783-0

SSG: 11

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Characterizing the Major Structural Variant Alleles of the Human Genome

Audano, Peter A. ; Sulovari, Arvis ; Graves-Lindsay, Tina A. ; [et al.]

Elsevier BV ; 2019

In: Cell Vol. 176, No. 3 ( 2019-01), p. 663-675.e19

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In: Cell, Elsevier BV, Vol. 176, No. 3 ( 2019-01), p. 663-675.e19

Type of Medium: Online Resource

ISSN: 0092-8674

URL: Article

DOI: 10.1016/j.cell.2018.12.019

RVK:

XA 36269

RVK:

WA 15000

Language: English

Publisher: Elsevier BV

Publication Date: 2019

detail.hit.zdb_id: 187009-9

detail.hit.zdb_id: 2001951-8

SSG: 12

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Comprehensive Analysis of Copy Number Variation of Genes at Chromosome 1 and 10 Loci Associated with Late Age Related Macular Degeneration

Cantsilieris, Stuart ; White, Stefan J. ; Richardson, Andrea J. ; [et al.]

Public Library of Science (PLoS) ; 2012

In: PLoS ONE Vol. 7, No. 4 ( 2012-4-25), p. e35255-

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In: PLoS ONE, Public Library of Science (PLoS), Vol. 7, No. 4 ( 2012-4-25), p. e35255-

Type of Medium: Online Resource

ISSN: 1932-6203

URL: Article

DOI: 10.1371/journal.pone.0035255

DOI: 10.1371/journal.pone.0035255.g001

DOI: 10.1371/journal.pone.0035255.g002

DOI: 10.1371/journal.pone.0035255.t001

DOI: 10.1371/journal.pone.0035255.t002

DOI: 10.1371/journal.pone.0035255.t003

DOI: 10.1371/journal.pone.0035255.s001

DOI: 10.1371/journal.pone.0035255.s002

DOI: 10.1371/journal.pone.0035255.s003

DOI: 10.1371/journal.pone.0035255.s004

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2012

detail.hit.zdb_id: 2267670-3

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Genomic inversions and GOLGA core duplicons underlie disease instability at the 15q25 locus

Maggiolini, Flavia A. M. ; Cantsilieris, Stuart ; D’Addabbo, Pietro ; [et al.]

Public Library of Science (PLoS) ; 2019

In: PLOS Genetics Vol. 15, No. 3 ( 2019-3-27), p. e1008075-

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In: PLOS Genetics, Public Library of Science (PLoS), Vol. 15, No. 3 ( 2019-3-27), p. e1008075-

Type of Medium: Online Resource

ISSN: 1553-7404

URL: Article

DOI: 10.1371/journal.pgen.1008075

DOI: 10.1371/journal.pgen.1008075.g001

DOI: 10.1371/journal.pgen.1008075.g002

DOI: 10.1371/journal.pgen.1008075.g003

DOI: 10.1371/journal.pgen.1008075.g004

DOI: 10.1371/journal.pgen.1008075.g005

DOI: 10.1371/journal.pgen.1008075.t001

DOI: 10.1371/journal.pgen.1008075.s001

DOI: 10.1371/journal.pgen.1008075.s002

DOI: 10.1371/journal.pgen.1008075.s003

DOI: 10.1371/journal.pgen.1008075.s004

DOI: 10.1371/journal.pgen.1008075.s005

DOI: 10.1371/journal.pgen.1008075.s006

DOI: 10.1371/journal.pgen.1008075.s007

DOI: 10.1371/journal.pgen.1008075.s008

DOI: 10.1371/journal.pgen.1008075.s009

DOI: 10.1371/journal.pgen.1008075.s010

DOI: 10.1371/journal.pgen.1008075.s011

DOI: 10.1371/journal.pgen.1008075.s012

Language: English

Publisher: Public Library of Science (PLoS)

Publication Date: 2019

detail.hit.zdb_id: 2186725-2

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