Multi-modal investigation of the schizophrenia-associated 3q29 genomic interval reveals global genetic diversity with unique haplotypes and segments that increase the risk for non-allelic homologous recombination

Chromosomal rearrangements that alter the copy number of dosage-sensitive genes can result in genomic disorders, such as the 3q29 deletion syndrome. At the 3q29 region, non-allelic homologous recombination (NAHR) between paralogous copies of segmental duplications (SDs) leads to a recurrent ~1.6 Mbp deletion or duplication, causing neurodevelopmental and psychiatric phenotypes. However, risk factors contributing to NAHR at this locus are not well understood. In this study, we used an optical mapping approach to identify structural variations within the 3q29 interval. We identified 18 novel haplotypes among 161 unaffected individuals and used this information to characterize this region in 18 probands with either the 3q29 deletion or 3q29 duplication syndrome. A significant amount of variation in haplotype prevalence was observed between populations. Within probands, we narrowed down the breakpoints to a ~5 kbp segment within the SD blocks in 89% of the 3q29 deletion and duplication cases studied. Furthermore, all 3q29 deletion and duplication cases could be categorized into one of five distinct classes based on their breakpoints. Contrary to previous findings for other recurrent deletion and duplication loci, there was no evidence for inversions in either parent of the probands mediating the deletion or duplication seen in this syndrome.

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A recurrent deletion syndrome at chromosome bands 2p11.2-2p12 flanked by segmental duplications at the breakpoints and including REEP1

European Journal of Human Genetics ◽

10.1038/ejhg.2014.124 ◽

2014 ◽

Vol 23 (4) ◽

pp. 543-546 ◽

Cited By ~ 6

Author(s):

Servi J C Stevens ◽

Eveline W Blom ◽

Ingrid T J Siegelaer ◽

Eric E J G L Smeets

Keyword(s):

Deletion Syndrome ◽

Segmental Duplications ◽

Chromosome Bands ◽

Recurrent Deletion

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A new experimental system to study meiotic recurrent non-allelic homologous recombination in budding yeast

10.1101/2020.06.25.164855 ◽

2020 ◽

Author(s):

Hailey N. C. Sedam ◽

Juan Lucas Argueso

Keyword(s):

Homologous Recombination ◽

Copy Number ◽

De Novo ◽

Chromosomal Rearrangements ◽

Experimental System ◽

Single Copy ◽

Copy Number Variations ◽

Repeat Elements ◽

Promising Tool ◽

Recombination Pathway

ABSTRACTIn humans, de novo recurrent copy number variations (CNVs) often arise during meiosis from non-allelic homologous recombination (NAHR) between low copy repeat elements (LCRs). These chromosomal rearrangements are responsible for a wide variety of genomic disorders involving duplication or deletion of dose-sensitive genes. The precise factors that steer meiotic cells toward this detrimental recombination pathway are not fully understood. To create a model for the investigation of LCR-mediated CNV mechanisms, we developed a diploid experimental system in Saccharomyces cerevisiae. We modified the right arm of chromosome V through the introduction of engineered LCRs: duplicated 5 to 35 kb segments of yeast DNA flanking single copy interstitial spacers, analogously to the meiotic NAHR substrates that exist in humans. Phenotypic markers, including a copy number reporter, were inserted within the interstitial spacer. Their segregation in the haploid meiotic progeny was used to phenotypically identity and classify recurrent CNV events. This system allowed us to measure the effects of LCR size on the frequency of meiotic de novo recurrent CNV formation, and to determine the relative proportions of each of the three main NAHR classes: interhomolog, intersister, and intrachromatid. The frequency of CNV increased as the LCRs became larger, and interhomolog NAHR was overrepresented relative to the two other classes. We showed that this experimental system directly mimics the features of de novo recurrent CNVs reported in human disease, thus it represents a promising tool for the discovery and characterization of conserved cellular factors and environmental exposures that can modulate meiotic NAHR.

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Genome mapping resolves structural variation within segmental duplications associated with microdeletion/microduplication syndromes

10.1101/2020.04.30.071449 ◽

2020 ◽

Author(s):

Yulia Mostovoy ◽

Feyza Yilmaz ◽

Stephen K. Chow ◽

Catherine Chu ◽

Chin Lin ◽

...

Keyword(s):

Single Molecule ◽

Structural Variation ◽

Optical Mapping ◽

Genome Mapping ◽

Sequence Similarity ◽

Chromosomal Rearrangements ◽

Population Level ◽

Segmental Duplications ◽

Microdeletion Syndromes ◽

Genomic Disorders

AbstractSegmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. These three genomic regions, and the SDs within them, have been previously analyzed in a small number of individuals. However, population-level studies have been lacking because most techniques used for analyzing these complex regions are both labor- and cost-intensive. In this study, we present a high-throughput technique to genotype complex structural variation using a single molecule, long-range optical mapping approach. We identified novel structural variants (SVs) at 7q11.23, 15q13.3 and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising 5 super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we refined the microdeletion breakpoints located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.

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Comparison of Karyotypes in Two Hybridizing Passerine Species: Conserved Chromosomal Structure but Divergence in Centromeric Repeats

Frontiers in Genetics ◽

10.3389/fgene.2021.768987 ◽

2021 ◽

Vol 12 ◽

Author(s):

Manon Poignet ◽

Martina Johnson Pokorná ◽

Marie Altmanová ◽

Zuzana Majtánová ◽

Dmitry Dedukh ◽

...

Keyword(s):

Copy Number ◽

Chromosomal Rearrangements ◽

Repetitive Sequences ◽

Chromosome Morphology ◽

Comparative Genomic ◽

Structural Variations ◽

Chromosomal Structure ◽

Meiotic Chromosomes ◽

Passerine Species ◽

Number Variation

Changes in chromosomal structure involving chromosomal rearrangements or copy number variation of specific sequences can play an important role in speciation. Here, we explored the chromosomal structure of two hybridizing passerine species; the common nightingale (Luscinia megarhynchos) and the thrush nightingale (Luscinia luscinia), using conventional cytogenetic approaches, immunostaining of meiotic chromosomes, fluorescence in situ hybridization as well as comparative genomic hybridization (CGH). We found that the two nightingale species show conserved karyotypes with the same diploid chromosome number of 2n = 84. In addition to standard chromosomes, both species possessed a small germline restricted chromosome of similar size as a microchromosome. Just a few subtle changes in chromosome morphology were observed between the species, suggesting that only a limited number of chromosomal rearrangements occurred after the species divergence. The interspecific CGH experiment suggested that the two nightingale species might have diverged in centromeric repetitive sequences in most macro- and microchromosomes. In addition, some chromosomes showed changes in copy number of centromeric repeats between the species. The observation of very similar karyotypes in the two nightingale species is consistent with a generally slow rate of karyotype evolution in birds. The divergence of centromeric sequences between the two species could theoretically cause meiotic drive or reduced fertility in interspecific hybrids. Nevertheless, further studies are needed to evaluate the potential role of chromosomal structural variations in nightingale speciation.

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Haplotype-resolved inversion landscape reveals hotspots of mutational recurrence associated with genomic disorders

10.1101/2021.12.20.472354 ◽

2021 ◽

Author(s):

David Porubsky ◽

Wolfram Höps ◽

Hufsah Ashraf ◽

PingHsun Hsieh ◽

Bernardo Rodriguez-Martin ◽

...

Keyword(s):

Copy Number ◽

Copy Number Variants ◽

Segmental Duplications ◽

Common Variants ◽

Base Pairs ◽

Genomic Technologies ◽

Human Genomes ◽

Heterozygous Carriers ◽

Critical Regions ◽

Genomic Disorders

Unlike copy number variants (CNVs), inversions remain an underexplored genetic variation class. By integrating multiple genomic technologies, we discover 729 inversions in 41 human genomes. Approximately 85% of inversions <2 kbp form by twin-priming during L1-retrotransposition; 80% of the larger inversions are balanced and affect twice as many base pairs as CNVs. Balanced inversions show an excess of common variants, and 72% are flanked by segmental duplications (SDs) or mobile elements. Since this suggests recurrence due to non-allelic homologous recombination, we developed complementary approaches to identify recurrent inversion formation. We describe 40 recurrent inversions encompassing 0.6% of the genome, showing inversion rates up to 2.7*10-4 per locus and generation. Recurrent inversions exhibit a sex-chromosomal bias, and significantly co-localize to the critical regions of genomic disorders. We propose that inversion recurrence results in an elevated number of heterozygous carriers and structural SD diversity, which increases mutability in the population and predisposes to disease-causing CNVs.

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Evidence for opposing selective forces operating on human-specific duplicated TCAF genes in Neanderthals and humans

Nature Communications ◽

10.1038/s41467-021-25435-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

PingHsun Hsieh ◽

Vy Dang ◽

Mitchell R. Vollger ◽

Yafei Mao ◽

Tzu-Hsueh Huang ◽

...

Keyword(s):

Copy Number ◽

Homo Sapiens ◽

Segmental Duplications ◽

Sensor Protein ◽

Long Read ◽

Number Variation ◽

Selective Forces ◽

Structural Mutations ◽

Cold Sensor ◽

Human Specific

AbstractTRP channel-associated factor 1/2 (TCAF1/TCAF2) proteins antagonistically regulate the cold-sensor protein TRPM8 in multiple human tissues. Understanding their significance has been complicated given the locus spans a gap-ridden region with complex segmental duplications in GRCh38. Using long-read sequencing, we sequence-resolve the locus, annotate full-length TCAF models in primate genomes, and show substantial human-specific TCAF copy number variation. We identify two human super haplogroups, H4 and H5, and establish that TCAF duplications originated ~1.7 million years ago but diversified only in Homo sapiens by recurrent structural mutations. Conversely, in all archaic-hominin samples the fixation for a specific H4 haplotype without duplication is likely due to positive selection. Here, our results of TCAF copy number expansion, selection signals in hominins, and differential TCAF2 expression between haplogroups and high TCAF2 and TRPM8 expression in liver and prostate in modern-day humans imply TCAF diversification among hominins potentially in response to cold or dietary adaptations.

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PATH-17. INTRAGENIC COPY NUMBER BREAKPOINT ANALYSIS OF METHYLATION DATA FROM CNS TUMOURS IDENTIFIES NOVEL SUBGROUP-SPECIFIC CANDIDATE FUSION GENE ENRICHMENTS

Neuro-Oncology ◽

10.1093/neuonc/noaa222.652 ◽

2020 ◽

Vol 22 (Supplement_3) ◽

pp. iii427-iii428

Author(s):

Alan Mackay ◽

Yura Grabovska ◽

Matthew Clarke ◽

Diana Carvalho ◽

Sara Temelso ◽

...

Keyword(s):

Copy Number ◽

Fusion Gene ◽

High Grade Glioma ◽

Structural Variations ◽

Methylation Array ◽

Kinase Gene ◽

Integrated Diagnosis ◽

Cns Tumours ◽

Breakpoint Analysis ◽

Balanced Translocations

Abstract Methylation array-based molecular profiling has redefined the classification of brain tumours and now forms an important part of their integrated diagnosis, providing both subgroup assignment and genome wide DNA copy number profiles. These latter data can be used to identify intragenic breakpoints which are frequently associated with structural variations resulting in therapeutically targetable oncogenic fusion genes. To systematically assess the landscape of these alterations, we combined publicly available methylation datasets resulting in a total of 5660 CNS tumours, around half paediatric, and including >1000 high grade glioma and DIPG. These were analysed by standard methodology (MNP, conumee), and intragenic breakpoint enrichment was compared within methylation subgroups, superfamilies, and tumours with no high-scoring classification. Benchmarking included sequence-verified cases such as infant hemispheric gliomas (IHG) with ALK(15%) and ROS1(7%) fusions, and pathognomic alterations associated with specific entities such as RELA-EPN, MYB-LGG and HGNET-MN1. We identified previously unreported enrichments of well-recognised fusion targets such as NTRK2in GBM_MID and NTRK3in DMG_K27 (both 5%), METin A_IDH / A_IDH_HG (3–5%), and FGFR1/3in GBM_G34 (8–9%). Novel recurrent kinase gene candidates to be verified and explored further include IGF1Rin 2–12% cases spanning glioma subgroups, and TIE1in poorly classified tumours. This latter ‘NOS’ group were also enriched in various transcription factor targets of breakpoints, including TCF4and PLAGL2. Despite limitations due to sample quality, resolution or balanced translocations, breakpoint analysis of methylation copy number profiles provides simple screening for structural rearrangements which may directly influence targeted therapy in paediatric CNS tumours.

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HiCancer: accurate and complete cancer genome phasing with Hi-C reads

Scientific Reports ◽

10.1038/s41598-021-86104-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Weihua Pan ◽

Desheng Gong ◽

Da Sun ◽

Haohui Luo

Keyword(s):

Copy Number ◽

Somatic Mutations ◽

Copy Number Variations ◽

Cancer Genome ◽

Structural Variations ◽

Genome Map ◽

Linkage Information ◽

Suboptimal Solution ◽

Allelic Copy Number ◽

Very High

AbstractDue to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.

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Genomic alterations caused by HPV integration in a cohort of Chinese endocervical adenocarcinomas

Cancer Gene Therapy ◽

10.1038/s41417-020-00283-4 ◽

2021 ◽

Author(s):

Wenhui Li ◽

Wanjun Lei ◽

Xiaopei Chao ◽

Xiaochen Song ◽

Yalan Bi ◽

...

Keyword(s):

Copy Number ◽

Somatic Mutations ◽

Hpv Infection ◽

Copy Number Variations ◽

Cervical Adenocarcinoma ◽

Structural Variations ◽

Driver Genes ◽

Genetic Changes ◽

Genomic Changes ◽

Whole Exome

AbstractThe association between human papillomavirus (HPV) integration and relevant genomic changes in uterine cervical adenocarcinoma is poorly understood. This study is to depict the genomic mutational landscape in a cohort of 20 patients. HPV+ and HPV− groups were defined as patients with and without HPV integration in the host genome. The genetic changes between these two groups were described and compared by whole-genome sequencing (WGS) and whole-exome sequencing (WES). WGS identified 2916 copy number variations and 743 structural variations. WES identified 6113 somatic mutations, with a mutational burden of 2.4 mutations/Mb. Six genes were predicted as driver genes: PIK3CA, KRAS, TRAPPC12, NDN, GOLGA6L4 and BAIAP3. PIK3CA, NDN, GOLGA6L4, and BAIAP3 were recognized as significantly mutated genes (SMGs). HPV was detected in 95% (19/20) of patients with cervical adenocarcinoma, 7 of whom (36.8%) had HPV integration (HPV+ group). In total, 1036 genes with somatic mutations were confirmed in the HPV+ group, while 289 genes with somatic mutations were confirmed in the group without HPV integration (HPV− group); only 2.1% were shared between the two groups. In the HPV+ group, GOLGA6L4 and BAIAP3 were confirmed as SMGs, while PIK3CA, NDN, KRAS, FUT1, and GOLGA6L64 were identified in the HPV− group. ZDHHC3, PKD1P1, and TGIF2 showed copy number amplifications after HPV integration. In addition, the HPV+ group had significantly more neoantigens. HPV integration rather than HPV infection results in different genomic changes in cervical adenocarcinoma.

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RAD6 Promotes Homologous Recombination Repair by Activating the Autophagy-Mediated Degradation of Heterochromatin Protein HP1

Molecular and Cellular Biology ◽

10.1128/mcb.01044-14 ◽

2014 ◽

Vol 35 (2) ◽

pp. 406-416 ◽

Cited By ~ 26

Author(s):

Su Chen ◽

Chen Wang ◽

Luxi Sun ◽

Da-Liang Wang ◽

Lu Chen ◽

...

Keyword(s):

Homologous Recombination ◽

Genome Stability ◽

Chromosomal Rearrangements ◽

Strand Break ◽

Open Chromatin ◽

Dsb Repair ◽

Heterochromatin Protein ◽

Dna Double Strand Break ◽

Recombination Repair ◽

Ubiquitin Conjugating Enzyme

Efficient DNA double-strand break (DSB) repair is critical for the maintenance of genome stability. Unrepaired or misrepaired DSBs cause chromosomal rearrangements that can result in severe consequences, such as tumorigenesis. RAD6 is an E2 ubiquitin-conjugating enzyme that plays a pivotal role in repairing UV-induced DNA damage. Here, we present evidence that RAD6 is also required for DNA DSB repair via homologous recombination (HR) by specifically regulating the degradation of heterochromatin protein 1α (HP1α). Our study indicates that RAD6 physically interacts with HP1α and ubiquitinates HP1α at residue K154, thereby promoting HP1α degradation through the autophagy pathway and eventually leading to an open chromatin structure that facilitates efficient HR DSB repair. Furthermore, bioinformatics studies have indicated that the expression of RAD6 and HP1α exhibits an inverse relationship and correlates with the survival rate of patients.

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