Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families
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Mendeley | Further Information

{"title"=>"Haplotype phasing and inheritance of copy number variants in nuclear families", "type"=>"journal", "authors"=>[{"first_name"=>"Priit", "last_name"=>"Palta", "scopus_author_id"=>"23012599400"}, {"first_name"=>"Lauris", "last_name"=>"Kaplinski", "scopus_author_id"=>"8516126400"}, {"first_name"=>"Liina", "last_name"=>"Nagirnaja", "scopus_author_id"=>"8966024700"}, {"first_name"=>"Andres", "last_name"=>"Veidenberg", "scopus_author_id"=>"36697505800"}, {"first_name"=>"Märt", "last_name"=>"Möls", "scopus_author_id"=>"6602364118"}, {"first_name"=>"Mari", "last_name"=>"Nelis", "scopus_author_id"=>"57194094862"}, {"first_name"=>"Tõnu", "last_name"=>"Esko", "scopus_author_id"=>"26648246800"}, {"first_name"=>"Andres", "last_name"=>"Metspalu", "scopus_author_id"=>"7004697483"}, {"first_name"=>"Maris", "last_name"=>"Laan", "scopus_author_id"=>"7004351459"}, {"first_name"=>"Maido", "last_name"=>"Remm", "scopus_author_id"=>"6603479527"}], "year"=>2015, "source"=>"PLoS ONE", "identifiers"=>{"pui"=>"604108641", "sgr"=>"84928905468", "issn"=>"19326203", "pmid"=>"25853576", "scopus"=>"2-s2.0-84928905468", "doi"=>"10.1371/journal.pone.0122713"}, "id"=>"ea457319-5fa3-3999-88ef-97ad23f66ae7", "abstract"=>"DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called PiCNV, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, PiCNV enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several de novo deletions and duplications in the offspring.", "link"=>"http://www.mendeley.com/research/haplotype-phasing-inheritance-copy-number-variants-nuclear-families", "reader_count"=>24, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Researcher"=>3, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>2, "Student > Master"=>7, "Other"=>1, "Student > Bachelor"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>1, "Biochemistry, Genetics and Molecular Biology"=>6, "Mathematics"=>1, "Agricultural and Biological Sciences"=>14, "Medicine and Dentistry"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>14}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>6}, "Mathematics"=>{"Mathematics"=>1}, "Unspecified"=>{"Unspecified"=>1}}, "reader_count_by_country"=>{"Germany"=>1, "Spain"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/2010113"], "description"=>"<p>In case informative polymorphic genotypes are present <i>between</i> haplotypes in an individual, copy number gain-carrying haplotypes (cn>1) can be deterministically distinguished from the normal single copy haplotypes (cn = 1). Furthermore, these informative genotypes can be used to establish the allelic composition and different allelic copies <i>within</i> copy number gain-carrying haplotypes.</p><p>CNV regions in HapMap YRI and EGCUT parents where allelic variability between and within normal and copy number gain-carrying haplotypes can be deterministically differentiated.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371469, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.t004", "stats"=>{"downloads"=>3, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_CNV_regions_in_HapMap_YRI_and_EGCUT_parents_where_allelic_variability_between_and_within_normal_and_copy_number_gain_carrying_haplotypes_can_be_deterministically_differentiated_/1371469", "title"=>"CNV regions in HapMap YRI and EGCUT parents where allelic variability between and within normal and copy number gain-carrying haplotypes can be deterministically differentiated.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010112"], "description"=>"<p>*Statistically significant (multiple-testing corrected p-value<0.05) deviations from the expected Mendelian transmission rate of 50%.</p><p>Transmission rate together with the number of transmitted variant-carrying haplotypes and the number of all transmission events (1 event/per locus/per child) for each of the non-overlapping CNV length intervals.</p><p>Transmission rate of deletion- and duplication-carrying haplotypes in HapMap YRI and EGCUT datasets combined.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371468, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.t003", "stats"=>{"downloads"=>8, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Transmission_rate_of_deletion_and_duplication_carrying_haplotypes_in_HapMap_YRI_and_EGCUT_datasets_combined_/1371468", "title"=>"Transmission rate of deletion- and duplication-carrying haplotypes in HapMap YRI and EGCUT datasets combined.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010109"], "description"=>"<p>(<b>A</b>) <i>De novo</i> arisen 67 kb-long deletion on chromosome 6:80596173–80663256 in family T39. Children 1–3 (C010135, C010136 and C010137) have inherited one normal haplotype from both parents. One child (Child 4, C010138) has inherited one normal haplotype from his mother (C010134) and a paternal haplotype with a <i>de novo</i> deletion event in the corresponding region. (<b>B</b>) <i>De novo</i> arisen 167 kb-long duplication on chromosome 2:110175122–110331912 in family T07. The only child (C010026) has inherited one normal haplotype from her mother (C010025) and a paternal haplotype with a <i>de novo</i> intra-chromosomal duplication event in the corresponding region. Coloured arrows show the transmission of specific haplotypes from parents to offspring in a given CNV region. Respective B-allele frequency (BAF, upper panel) and total fluorescent signal intensity (Log R Ratio—LRR, lower panel) plots from Illumina Genome Viewer are shown next to the parents and each child.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371465, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.g004", "stats"=>{"downloads"=>1, "page_views"=>20, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_de_novo_copy_number_variants_in_offspring_/1371465", "title"=>"Examples of <i>de novo</i> copy-number variants in offspring.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010107"], "description"=>"<p>(<b>A</b>) First, CNV and regular two-letter genotypes are collected from the QuantiSNP output for each family member at a locus of interest. (<b>B</b>) Next, markers that have any low-confidence genotype calls or the call could not have been made (‘NC’ genotypes, e.g. marker rs10801575, marked with the red background) and monomorphic markers that are not informative for haplotype phasing in the studied region (e.g. marker rs7517836; marked with the red background) are filtered out. (<b>C</b>) Informative high-confidence genotypes are then phased considering all family members simultaneously and the resulting haplotypes are presented as the result. (<b>D</b>) The family tree of these phased haplotypes can be further visualised for the corresponding CNV region.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371463, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.g002", "stats"=>{"downloads"=>4, "page_views"=>11, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Computational_phasing_of_normal_and_CNV_carrying_haplotypes_/1371463", "title"=>"Computational phasing of normal and CNV-carrying haplotypes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010108"], "description"=>"<p>(<b>A</b>) Inherited 820 kb-long deletion on chromosome 16:15369798–16190572 in family T3. A deletion-carrying haplotype (cn = 0) is inherited from father (C010008) to son (Child 2, C010010). The daughter (Child 1, C010011) has inherited normal haplotypes (cn = 1) from both parents. (<b>B</b>) Inherited 166 kb-long duplication on chromosome 10:47007374–47173619 in family T14. A duplication-carrying haplotype (cn = 2) is inherited from father (C010046) to one son (Child 1, C010049) and daughter (Child 2, C010052). All other children have inherited normal haplotypes (cn = 1) from both parents. Coloured arrows show the transmission of specific haplotypes from parents to offspring in a given CNV region. Respective B-allele frequency (BAF, upper panel) and total fluorescent signal intensity (Log R Ratio—LRR, lower panel) plots from Illumina Genome Viewer are shown next to the parents and each child.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371464, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.g003", "stats"=>{"downloads"=>2, "page_views"=>82, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Examples_of_unambiguously_phased_CNV_regions_involving_deletion_and_duplication_carrying_haplotypes_in_families_/1371464", "title"=>"Examples of unambiguously phased CNV regions involving deletion- and duplication-carrying haplotypes in families.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010106"], "description"=>"<p>A chromosomal region involving copy number variation is denoted with ‘R2’. In the given example, father is the carrier of two normal haplotypes of ‘R2’ on chromosomes P1 and P2 (diploid copy number of ‘R2’, CN = 2), whereas mother has a combination of a duplication-carrying (on M1) and normal (M2) haplotypes (diploid copy number of ‘R2’, CN = 3). Haplotype-informative SNP genotypes in ‘R2’ sequence that can be used for phasing and determining the parental origin (in offspring) of given normal and CNV-carrying haplotypes are given in bold letters and genotypes that are polymorphic <i>between</i> normal or duplication-carrying parental haplotypes are indicated with dashed rectangles. The duplication-carrying haplotype on maternal M1 chromosome is composed of two allelic copies of the sequence ‘R2’ distinguished by genotype variability at position SNP7 (polymorphic SNP variant <i>within</i> the duplication-carrying haplotype), indicated with dotted rectangle.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371462, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.g001", "stats"=>{"downloads"=>0, "page_views"=>50, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Phasing_and_allelic_composition_of_normal_and_CNV_carrying_haplotypes_on_parental_homologous_chromosomes_/1371462", "title"=>"Phasing and allelic composition of normal and CNV-carrying haplotypes on parental homologous chromosomes.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010114", "https://ndownloader.figshare.com/files/2010115", "https://ndownloader.figshare.com/files/2010116", "https://ndownloader.figshare.com/files/2010117", "https://ndownloader.figshare.com/files/2010118", "https://ndownloader.figshare.com/files/2010119", "https://ndownloader.figshare.com/files/2010120"], "description"=>"<div><p>DNA copy number variants (CNVs) that alter the copy number of a particular DNA segment in the genome play an important role in human phenotypic variability and disease susceptibility. A number of CNVs overlapping with genes have been shown to confer risk to a variety of human diseases thus highlighting the relevance of addressing the variability of CNVs at a higher resolution. So far, it has not been possible to deterministically infer the allelic composition of different haplotypes present within the CNV regions. We have developed a novel computational method, called <i>PiCNV</i>, which enables to resolve the haplotype sequence composition within CNV regions in nuclear families based on SNP genotyping microarray data. The algorithm allows to i) phase normal and CNV-carrying haplotypes in the copy number variable regions, ii) resolve the allelic copies of rearranged DNA sequence within the haplotypes and iii) infer the heritability of identified haplotypes in trios or larger nuclear families. To our knowledge this is the first program available that can deterministically phase null, mono-, di-, tri- and tetraploid genotypes in CNV loci. We applied our method to study the composition and inheritance of haplotypes in CNV regions of 30 HapMap Yoruban trios and 34 Estonian families. For 93.6% of the CNV loci, <i>PiCNV</i> enabled to unambiguously phase normal and CNV-carrying haplotypes and follow their transmission in the corresponding families. Furthermore, allelic composition analysis identified the co-occurrence of alternative allelic copies within 66.7% of haplotypes carrying copy number gains. We also observed less frequent transmission of CNV-carrying haplotypes from parents to children compared to normal haplotypes and identified an emergence of several <i>de novo</i> deletions and duplications in the offspring.</p></div>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371470, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0122713.s001", "https://dx.doi.org/10.1371/journal.pone.0122713.s002", "https://dx.doi.org/10.1371/journal.pone.0122713.s003", "https://dx.doi.org/10.1371/journal.pone.0122713.s004", "https://dx.doi.org/10.1371/journal.pone.0122713.s005", "https://dx.doi.org/10.1371/journal.pone.0122713.s006", "https://dx.doi.org/10.1371/journal.pone.0122713.s007"], "stats"=>{"downloads"=>17, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Haplotype_Phasing_and_Inheritance_of_Copy_Number_Variants_in_Nuclear_Families_/1371470", "title"=>"Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010111"], "description"=>"<p>Percentage of CNV regions in HapMap YRI and EGCUT families where <i>PiCNV</i> was automatically able to unambiguously determine the underlying normal and CNV-carrying haplotypes in parents and follow their transmission in offspring. Group A—CNV regions where only one parent had a CNV; group B—CNV regions where both parents had a CNV in the same locus; group C—putative <i>de novo</i> CNV regions.</p><p>Unambiguously phased CNV regions in families.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371467, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.t002", "stats"=>{"downloads"=>7, "page_views"=>17, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Unambiguously_phased_CNV_regions_in_families_/1371467", "title"=>"Unambiguously phased CNV regions in families.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-08 03:00:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/2010110"], "description"=>"<p>Detailed description of analysed family-based SNP microarray datasets.</p>", "links"=>[], "tags"=>["copy number", "CNV regions", "Nuclear Families DNA copy number variants", "alternative allelic copies", "copy number variants", "haplotype sequence composition", "CNV loci", "SNP genotyping microarray data", "copy number gains", "allelic composition analysis", "30 HapMap Yoruban trios"], "article_id"=>1371466, "categories"=>["Uncategorised"], "users"=>["Priit Palta", "Lauris Kaplinski", "Liina Nagirnaja", "Andres Veidenberg", "Märt Möls", "Mari Nelis", "Tõnu Esko", "Andres Metspalu", "Maris Laan", "Maido Remm"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0122713.t001", "stats"=>{"downloads"=>4, "page_views"=>25, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Detailed_description_of_analysed_family_based_SNP_microarray_datasets_/1371466", "title"=>"Detailed description of analysed family-based SNP microarray datasets.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-04-08 03:00:00"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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