Haplotype Phasing and Inheritance of Copy Number Variants in Nuclear Families

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.Peer reviewe

Mechanistic insights into the evolution of DUF26-containing proteins in land plants

Large protein families are a prominent feature of plant genomes and their size variation is a key element for adaptation. However, gene and genome duplications pose difficulties for functional characterization and translational research. Here we infer the evolutionary history of the DOMAIN OF UNKNOWN FUNCTION (DUF) 26-containing proteins. The DUF26 emerged in secreted proteins. Domain duplications and rearrangements led to the appearance of CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASES (CRKs) and PLASMODESMATA-LOCALIZED PROTEINS (PDLPs). The DUF26 is land plant-specific but structural analyses of PDLP ectodomains revealed strong similarity to fungal lectins and thus may constitute a group of plant carbohydrate-binding proteins. CRKs expanded through tandem duplications and preferential retention of duplicates following whole genome duplications, whereas PDLPs evolved according to the dosage balance hypothesis. We propose that new gene families mainly expand through small-scale duplications, while fractionation and genetic drift after whole genome multiplications drive families towards dosage balance.Peer reviewe

Transmission rate of deletion- and duplication-carrying haplotypes in HapMap YRI and EGCUT datasets combined.

<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

Examples of unambiguously phased CNV regions involving deletion- and duplication-carrying haplotypes in families.

<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

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>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

Detailed description of analysed family-based SNP microarray datasets.

<p>Detailed description of analysed family-based SNP microarray datasets.</p

Phasing and allelic composition of normal and CNV-carrying haplotypes on parental homologous chromosomes.

<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