Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays

Genomic microarray analysis is rapidly replacing conventional chromosome analysis by molecular karyotyping due to the significant increase in the power to detect causative CNVs. Here, we extensively validated the HumanHap550 and Human610-Quadv1_B Illumina platforms for potential diagnostic applicati...

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Bibliographic Details
Author: Rivera Brugués, Núria
Format: doctoral thesis
Status:Published version
Publication Date:2012
Country:España
Institution:Universidad de Barcelona
Repository:Dipòsit Digital de la UB
OAI Identifier:oai:diposit.ub.edu:2445/41936
Online Access:https://hdl.handle.net/2445/41936
http://hdl.handle.net/10803/81745
Access Level:Open access
Keyword:Genoma humà
Oligonucleòtids
Microxips d'ADN
Human genome
Oligonucleotides
DNA microarrays
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oai_identifier_str oai:diposit.ub.edu:2445/41936
network_acronym_str ES
network_name_str España
repository_id_str
dc.title.none.fl_str_mv Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
title Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
spellingShingle Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
Rivera Brugués, Núria
Genoma humà
Oligonucleòtids
Microxips d'ADN
Human genome
Oligonucleotides
DNA microarrays
title_short Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
title_full Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
title_fullStr Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
title_full_unstemmed Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
title_sort Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarrays
dc.creator.none.fl_str_mv Rivera Brugués, Núria
author Rivera Brugués, Núria
author_facet Rivera Brugués, Núria
author_role author
dc.contributor.none.fl_str_mv Meitinger, Thomas
Vilageliu i Arqués, Lluïsa
Universitat de Barcelona. Departament de Genètica
dc.subject.none.fl_str_mv Genoma humà
Oligonucleòtids
Microxips d'ADN
Human genome
Oligonucleotides
DNA microarrays
topic Genoma humà
Oligonucleòtids
Microxips d'ADN
Human genome
Oligonucleotides
DNA microarrays
description Genomic microarray analysis is rapidly replacing conventional chromosome analysis by molecular karyotyping due to the significant increase in the power to detect causative CNVs. Here, we extensively validated the HumanHap550 and Human610-Quadv1_B Illumina platforms for potential diagnostic application by using patients with undiagnosed intellectual disability (ID). The first and foremost goal of our application study was to use these arrays for reliable genome wide detection of rare CNVs in patients of three different cohorts: 1) patients with unexplained intellectual disability 2) patients with unknown diffuse congenital hyperinsulinism (CHI) and 3) a family with a distinctive diagnosis of Holt-Oram syndrome (HOS). We showed that SNP-based arrays allow the detection of intragenic deletions and duplications. The identification of a disease-CNV affecting only a single gene allowed us to consider that particular gene as a candidate for intellectual disability. This was the case for three unrelated patients with moderate intellectual disability, global developmental delay, and severe speech and language disorders in which a de novo deletion encompassing solely the FOXP1 gene was detected. To prove further the causality of the FOXP1 deletion following-up investigations were based on a screening of the entire coding region of FOXP1 for nucleotide changes in a panel of 883 probands with intellectual disability. Eight non-synonymous coding changes, three synonymous and nine non-coding variants were identified. In addition to the de novo cases of ID, also patients suffering from an autosomal recessive form of ID were found in our cohort. We detected three partial heterozygous deletions of the COH1 gene at locus 8q22 which is mutated in Cohen syndrome. After sequencing the entire coding region and the exon/intron boundaries of COH1 we identified a stop mutation, a frameshift and two missense mutations in the remaining allele, respectively. Therefore, three compound heterozygous mutations were identified in the COH1 gene, thus providing a distinctive Cohen Syndrome diagnose to three unrelated patients of our ID cohort. We studied the genetic basis of a rare human autosomal disorder such as diffuse Congenital Hyperinsulinsm (CHI) in a cohort of 40 patients with inconspicuous mutation screening of ABCC8 and KCNJ11 genes. Chromosomal abnormalities detected by SNP oligonucleotide arrays accounted for 20% of the studied cases. The most interesting rearrangement was a 970kb deletion at the chromosomal band 1p31.1 which was found to encompass the PTGER3 and ZRANB2 genes and the last exon of the NEGR1 gene. We hypothesized that the haploinsufficiency of PTGER3 gene induces a 50% reduction of the stimulation by PGE2, thus diminishing the inhibition of glucose-stimulated insulin secretion (GSIS) and resulting in elevated insulin secretion. The screening for point mutations in the candidate gene PTGER3 did not reveal any pathogenic variant neither in the second allele of the patient in which a de novo deletion was detected nor in a cohort of 39 unrelated patients with unexplained CHI. Instead we identified a novel polymorphic variant which was also detected in 18 individuals of our control cohort. CNV analysis in a family with both atypical Holt-Oram syndrome and additional mammary glands was performed allowing the detection of a contiguous heterozygous duplication at the chromosomal band 12q24.21. The maximal duplication size could be estimated as aproximately 345,6kb including the whole coding region of the TBX5 and TBX3 genes. Gene dosage assessment at specific genetic loci demonstrated the cosegregation of the duplication and the Holt-Oram syndrome/supernumerary mammary glands phenotype in this pedigree, this being a strong indicator of its pathogenecity. Up to date, this is the first report of a heterozygous duplication encompassing both TBX5 and TBX3 genes, and consequently the first report of a combined phenotype of Holt-Oram syndrome and supernumerary mammary glands.
publishDate 2012
dc.date.none.fl_str_mv 2012
dc.type.none.fl_str_mv info:eu-repo/semantics/doctoralThesis
info:eu-repo/semantics/publishedVersion
format doctoralThesis
status_str publishedVersion
dc.identifier.none.fl_str_mv https://hdl.handle.net/2445/41936
http://hdl.handle.net/10803/81745
url https://hdl.handle.net/2445/41936
http://hdl.handle.net/10803/81745
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.rights.none.fl_str_mv (c) Rivera Brugués, 2012
info:eu-repo/semantics/openAccess
rights_invalid_str_mv (c) Rivera Brugués, 2012
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Universitat de Barcelona
publisher.none.fl_str_mv Universitat de Barcelona
dc.source.none.fl_str_mv Tesis Doctorals - Departament - Genètica
reponame:Dipòsit Digital de la UB
instname:Universidad de Barcelona
instname_str Universidad de Barcelona
reponame_str Dipòsit Digital de la UB
collection Dipòsit Digital de la UB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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spelling Identification and characterization of disease-related copy number variations (CNVs) by high-dense SNP oligonucleotide microarraysRivera Brugués, NúriaGenoma humàOligonucleòtidsMicroxips d'ADNHuman genomeOligonucleotidesDNA microarraysGenomic microarray analysis is rapidly replacing conventional chromosome analysis by molecular karyotyping due to the significant increase in the power to detect causative CNVs. Here, we extensively validated the HumanHap550 and Human610-Quadv1_B Illumina platforms for potential diagnostic application by using patients with undiagnosed intellectual disability (ID). The first and foremost goal of our application study was to use these arrays for reliable genome wide detection of rare CNVs in patients of three different cohorts: 1) patients with unexplained intellectual disability 2) patients with unknown diffuse congenital hyperinsulinism (CHI) and 3) a family with a distinctive diagnosis of Holt-Oram syndrome (HOS). We showed that SNP-based arrays allow the detection of intragenic deletions and duplications. The identification of a disease-CNV affecting only a single gene allowed us to consider that particular gene as a candidate for intellectual disability. This was the case for three unrelated patients with moderate intellectual disability, global developmental delay, and severe speech and language disorders in which a de novo deletion encompassing solely the FOXP1 gene was detected. To prove further the causality of the FOXP1 deletion following-up investigations were based on a screening of the entire coding region of FOXP1 for nucleotide changes in a panel of 883 probands with intellectual disability. Eight non-synonymous coding changes, three synonymous and nine non-coding variants were identified. In addition to the de novo cases of ID, also patients suffering from an autosomal recessive form of ID were found in our cohort. We detected three partial heterozygous deletions of the COH1 gene at locus 8q22 which is mutated in Cohen syndrome. After sequencing the entire coding region and the exon/intron boundaries of COH1 we identified a stop mutation, a frameshift and two missense mutations in the remaining allele, respectively. Therefore, three compound heterozygous mutations were identified in the COH1 gene, thus providing a distinctive Cohen Syndrome diagnose to three unrelated patients of our ID cohort. We studied the genetic basis of a rare human autosomal disorder such as diffuse Congenital Hyperinsulinsm (CHI) in a cohort of 40 patients with inconspicuous mutation screening of ABCC8 and KCNJ11 genes. Chromosomal abnormalities detected by SNP oligonucleotide arrays accounted for 20% of the studied cases. The most interesting rearrangement was a 970kb deletion at the chromosomal band 1p31.1 which was found to encompass the PTGER3 and ZRANB2 genes and the last exon of the NEGR1 gene. We hypothesized that the haploinsufficiency of PTGER3 gene induces a 50% reduction of the stimulation by PGE2, thus diminishing the inhibition of glucose-stimulated insulin secretion (GSIS) and resulting in elevated insulin secretion. The screening for point mutations in the candidate gene PTGER3 did not reveal any pathogenic variant neither in the second allele of the patient in which a de novo deletion was detected nor in a cohort of 39 unrelated patients with unexplained CHI. Instead we identified a novel polymorphic variant which was also detected in 18 individuals of our control cohort. CNV analysis in a family with both atypical Holt-Oram syndrome and additional mammary glands was performed allowing the detection of a contiguous heterozygous duplication at the chromosomal band 12q24.21. The maximal duplication size could be estimated as aproximately 345,6kb including the whole coding region of the TBX5 and TBX3 genes. Gene dosage assessment at specific genetic loci demonstrated the cosegregation of the duplication and the Holt-Oram syndrome/supernumerary mammary glands phenotype in this pedigree, this being a strong indicator of its pathogenecity. Up to date, this is the first report of a heterozygous duplication encompassing both TBX5 and TBX3 genes, and consequently the first report of a combined phenotype of Holt-Oram syndrome and supernumerary mammary glands.Universitat de BarcelonaMeitinger, ThomasVilageliu i Arqués, LluïsaUniversitat de Barcelona. Departament de Genètica2012info:eu-repo/semantics/doctoralThesisinfo:eu-repo/semantics/publishedVersionapplication/pdfhttps://hdl.handle.net/2445/41936http://hdl.handle.net/10803/81745Tesis Doctorals - Departament - Genèticareponame:Dipòsit Digital de la UBinstname:Universidad de BarcelonaInglés(c) Rivera Brugués, 2012info:eu-repo/semantics/openAccessoai:diposit.ub.edu:2445/419362026-05-27T06:46:51Z
score 15,300719

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