Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models.

A large fraction of genome variation between individuals is comprised of submicroscopic copy number variation of genomic DNA segments. We assessed the relative contribution of structural changes and gene dosage alterations on phenotypic outcomes with mouse models of Smith-Magenis and Potocki-Lupski syndromes. We phenotyped mice with 1n (Deletion/+), 2n (+/+), 3n (Duplication/+), and balanced 2n compound heterozygous (Deletion/Duplication) copies of the same region. Parallel to the observations made in humans, such variation in gene copy number was sufficient to generate phenotypic consequences: in a number of cases diametrically opposing phenotypes were associated with gain versus loss of gene content. Surprisingly, some neurobehavioral traits were not rescued by restoration of the normal gene copy number. Transcriptome profiling showed that a highly significant propensity of transcriptional changes map to the engineered interval in the five assessed tissues. A statistically significant overrepresentation of the genes mapping to the entire length of the engineered chromosome was also found in the top-ranked differentially expressed genes in the mice containing rearranged chromosomes, regardless of the nature of the rearrangement, an observation robust across different cell lineages of the central nervous system. Our data indicate that a structural change at a given position of the human genome may affect not only locus and adjacent gene expression but also "genome regulation." Furthermore, structural change can cause the same perturbation in particular pathways regardless of gene dosage. Thus, the presence of a genomic structural change, as well as gene dosage imbalance, contributes to the ultimate phenotype.

Extreme degree of chromosome number variability in species of the spider genus Scytodes (Araneae, Haplogynae, Scytodidae)

Genus Scytodes includes most species of the spider family Scytodidae. Until now, 187 species of the genus have been described. In spite of this great diversity, only three Scytodes species were karyotyped so far. The present paper provides for the first time karyotype analysis of two synanthropic species, Scytodes fusca and Scytodes itapevi. Furthermore, new data on karyotype of Scytodes globula are also provided using conventional and differential cytogenetical procedures. The diploid number in the genus Scytodes varied considerably, namely from 2n = 13 to 2n = 31. The diploid number found in S. globula (2n male = 13) is the lowest in haplogyne spiders with monocentric chromosomes. Except S. globula, this number has been found only in one haplogyne spider with monocentric chromosomes, namely Ochyrocera sp. (Ochyroceratidae). on the contrary, the diploid number of S. fusca (2n male = 31) is one of the highest diploid numbers recorded in haplogyne spiders. The degree of intrageneric variation found in the genus Scytodes is the highest recorded in araneomorph spiders with monocentric chromosomes so far. Some karyotype characteristics (diploid number, chromosome morphology, total chromosome length, and distribution of constitutive heterochromatin) allowed us to postulate a close relationship between S. globula and S. itapevi. According to the karyotype data, S. fusca is not closely related to these two species. This conclusion corroborates a recent taxonomic work that grouped S. globula, S. itapevi, and other four Scytodes species in the 'globula group'.

Clinical relevance of polymorphic DNA copy number variation (CNV) in African American women with stage I-II breast cancer

Objectives. The chief goal of this study was to analyze copy number variation (CNV) in breast cancer tumors from 25 African American women with early stage breast cancer (BC) using molecular inversion probes (MIP) in order to: (1) compare the degree of CNV in tumors compared to normal lymph nodes, and (2) determine whether gains and/or losses of genes in specific chromosomes differ between pathologic subtypes of breast cancer defined by known prognostic markers, (3) determine whether gains/losses in CN are associated with known oncogenes or tumor suppressor genes, and (4) determine whether increased gains/losses in CN for specific chromosomes were associated with differences in breast cancer recurrence. ^ Methods. Twenty to 37 nanograms of DNA extracted from 25 formalin-fixed paraffin embedded (FFPE) tumor samples and matched normal lymph nodes were added to individual tubes. Oligonucleotide probes with recognition sequences at each terminus were hybridized with a genomic target sequence to form a circular structure. Probes are released from genomic DNA obtained from FFPE samples, and those which have been correctly "circularized" in the proper allele/nucleotide reaction combination are amplified using polymerase chain reaction (PCR) primers. Amplicons were fluorescently labeled and the tag sequences released from the genome homology regions by treatment with uracil-N-glycosylase to cleave the probe at the site where uracils are present, and detected using a complementary tag array developed by Affymetrix. ^ Results. Analysis of CN gains and losses from tumors and normal tissues showed marked differences in tumors with numerous chromosomes affected. Similar changes were not observed in normal lymph nodes. When tumors were stratified into four groups based on expression or lack of expression of the estrogen receptor and HER2/neu, distinct patterns of CNV for different chromosomes were observed. Gains or losses in CN for specific chromosomes correlated with amplifications/deletions of particular oncogenes or tumor suppressor genes (i.e. such as found on chromosome 17) known to be associated with aggressive tumor phenotype and poor prognosis. There was a trend for increases in CN observed for chromosome 17 to correlate inversely with time to recurrence of BC (p=0.14 for trend). CNV was also observed for chromosomes 5, 8, 10, 11, and 16, which are known sites for several breast cancer susceptibility alleles. ^ Conclusions. This study is the first to validate the MIP technique, to correlate differences in gene expression with known prognostic tumor markers, and to correlate significant increases/decreases in CN with known tumor markers associated with prognosis. The results of this study may have far reaching public health implications towards identifying new high-risk groups based on genomic differences in CNP, both with respect to prognosis and response to therapy, and to eventually identify new therapeutic targets for prevention and treatment of this disease. ^

Sorex bedfordiae has the Smallest Diploid Chromosome Number of the XY Group in the Genus Sorex (Mammalia, Soricidae)

Karyological data on the lesser stripe-backed shrew, Sorex bedfordiae, were obtained from four specimens collected on Mt. Laojun, Lijiang District, Yunnan Province, China. Three of the four S. bedfordiae specimens had karyotypes consisting of 2n=26, NFa=4

Quantitative Analysis of Single Nucleotide Polymorphisms within Copy Number Variation

Background Single nucleotide polymorphisms (SNPs) have been used extensively in genetics and epidemiology studies. Traditionally, SNPs that did not pass the Hardy-Weinberg equilibrium (HWE) test were excluded from these analyses. Many investigators have addressed possible causes for departure from HWE, including genotyping errors, population admixture and segmental duplication. Recent large-scale surveys have revealed abundant structural variations in the human genome, including copy number variations (CNVs). This suggests that a significant number of SNPs must be within these regions, which may cause deviation from HWE. Results We performed a Bayesian analysis on the potential effect of copy number variation, segmental duplication and genotyping errors on the behavior of SNPs. Our results suggest that copy number variation is a major factor of HWE violation for SNPs with a small minor allele frequency, when the sample size is large and the genotyping error rate is 0~1%. Conclusions Our study provides the posterior probability that a SNP falls in a CNV or a segmental duplication, given the observed allele frequency of the SNP, sample size and the significance level of HWE testing.

Genome-wide scan of copy number variation in late-onset Alzheimer's disease.

Alzheimer's disease is a complex and progressive neurodegenerative disease leading to loss of memory, cognitive impairment, and ultimately death. To date, six large-scale genome-wide association studies have been conducted to identify SNPs that influence disease predisposition. These studies have confirmed the well-known APOE epsilon4 risk allele, identified a novel variant that influences disease risk within the APOE epsilon4 population, found a SNP that modifies the age of disease onset, as well as reported the first sex-linked susceptibility variant. Here we report a genome-wide scan of Alzheimer's disease in a set of 331 cases and 368 controls, extending analyses for the first time to include assessments of copy number variation. In this analysis, no new SNPs show genome-wide significance. We also screened for effects of copy number variation, and while nothing was significant, a duplication in CHRNA7 appears interesting enough to warrant further investigation.

UNUSUAL CHROMOSOME-NUMBER OF GRACILARIA-VERRUCOSA (GRACILARIALES, RHODOPHYTA) IN THE CAPE-GRIS-NEZ AREA, NORTHERN FRANCE

The chromosome number of Gracilaria verrucosa (Hudson) Papenfuss was estimated in numerous individuals from different populations of the Cape Gris-Nez area of Northern France. To optimize estimates and to minimize counting errors, several counts were made on the same nucleus and in different nuclei of the same individual. The haploid chromosome number was estimated in vegetative gametophytic cells and tetrasporocytic cells; the diploid number was estimated from tetrasporophytic vegetative cells. The basic haploid number was n = 17 +/- 1, whereas all other Gracilaria species for which chromosome numbers are available are reported to have n = 24. These include populations of G. verrucosa from Norway and Wales that have previously been shown to be conspecific with the Cape Gris-Nez populations by comparison of plastid DNA data. G. verrucosa is therefore one of the few red algae for which populations with different chromosome numbers are known.

Copy number variation and Huntington’s disease

Tese de doutoramento, Ciências Biomédicas (Neurociências), Universidade de Lisboa, Faculdade de Medicina, 2014

X-chromosome genetic variation in São Paulo State (Brazil) population

As data on X-chromosomal short tandem repeats (X-STRs) for the Brazilian population are scarse, the aim of this study was to determine the allele frequencies of five X-STRs (DXS6854, DXS7424, DXS101, DXS6808 and DXS7132) in the São Paulo State, Brazil. No deviations from the Hardy-Weinberg equilibrium were observed, with the exception of DXS101. The forensic efficiency parameters demonstrated that DXS101 was the most informative marker. Population comparisons revealed that the X-STR profile sampled in the state of São Paulo was more similar to European and African populations than Asiatic populations reported in this work.

Description and chromosome number of a species of Pseudonannolene Silvestri (Arthropoda, Diplopoda, Pseudonannolenidae)

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.