@article {839, title = {Mapping and characterization of structural variation in 17,795 human genomes.}, journal = {Nature}, volume = {583}, year = {2020}, month = {2020 07}, pages = {83-89}, abstract = {

A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural variants. However, tools and resources for the study of structural variants have lagged behind those for smaller variants. Here we used a scalable pipeline to map and characterize structural variants in 17,795 deeply sequenced human genomes. We publicly release site-frequency data to create the largest, to our knowledge, whole-genome-sequencing-based structural variant resource so far. On average, individuals carry 2.9 rare structural variants that alter coding regions; these variants affect the dosage or structure of 4.2 genes and account for 4.0-11.2\% of rare high-impact coding alleles. Using a computational model, we estimate that structural variants account for 17.2\% of rare alleles genome-wide, with predicted deleterious effects that are equivalent to loss-of-function coding alleles; approximately 90\% of such structural variants are noncoding deletions (mean 19.1 per genome). We report 158,991 ultra-rare structural variants and show that 2\% of individuals carry ultra-rare megabase-scale structural variants, nearly half of which are balanced or complex rearrangements. Finally, we infer the dosage sensitivity of genes and noncoding elements, and reveal trends that relate to element class and conservation. This work will help to guide the analysis and interpretation of structural variants in the era of whole-genome sequencing.

}, keywords = {Alleles, Case-Control Studies, Continental Population Groups, Epigenesis, Genetic, Female, Gene Dosage, Genetic Variation, Genetics, Population, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Male, Molecular Sequence Annotation, Quantitative Trait Loci, Software, Whole Genome Sequencing}, issn = {1476-4687}, doi = {10.1038/s41586-020-2371-0}, author = {Abel, Haley J and Larson, David E and Regier, Allison A and Chiang, Colby and Das, Indraniel and Kanchi, Krishna L and Layer, Ryan M and Neale, Benjamin M and Salerno, William J and Reeves, Catherine and Buyske, Steven and Matise, Tara C and Muzny, Donna M and Zody, Michael C and Lander, Eric S and Dutcher, Susan K and Stitziel, Nathan O and Hall, Ira M} } @article {366, title = {Efficient CNV breakpoint analysis reveals unexpected structural complexity and correlation of dosage-sensitive genes with clinical severity in genomic disorders.}, journal = {Hum Mol Genet}, volume = {26}, year = {2017}, month = {2017 05 15}, pages = {1927-1941}, abstract = {

Genomic disorders are the clinical conditions manifested by submicroscopic genomic rearrangements including copy number variants (CNVs). The CNVs can be identified by array-based comparative genomic hybridization (aCGH), the most commonly used technology for molecular diagnostics of genomic disorders. However, clinical aCGH only informs CNVs in the probe-interrogated regions. Neither orientational information nor the resulting genomic rearrangement structure is provided, which is a key to uncovering mutational and pathogenic mechanisms underlying genomic disorders. Long-range polymerase chain reaction (PCR) is a traditional approach to obtain CNV breakpoint junction, but this method is inefficient when challenged by structural complexity such as often found at the PLP1 locus in association with Pelizaeus-Merzbacher disease (PMD). Here we introduced {\textquoteright}capture and single-molecule real-time sequencing{\textquoteright} (cap-SMRT-seq) and newly developed {\textquoteright}asymmetry linker-mediated nested PCR walking{\textquoteright} (ALN-walking) for CNV breakpoint sequencing in 49 subjects with PMD-associated CNVs. Remarkably, 29 (94\%) of the 31 CNV breakpoint junctions unobtainable by conventional long-range PCR were resolved by cap-SMRT-seq and ALN-walking. Notably, unexpected CNV complexities, including inter-chromosomal rearrangements that cannot be resolved by aCGH, were revealed by efficient breakpoint sequencing. These sequence-based structures of PMD-associated CNVs further support the role of DNA replicative mechanisms in CNV mutagenesis, and facilitate genotype-phenotype correlation studies. Intriguingly, the lengths of gained segments by CNVs are strongly correlated with clinical severity in PMD, potentially reflecting the functional contribution of other dosage-sensitive genes besides PLP1. Our study provides new efficient experimental approaches (especially ALN-walking) for CNV breakpoint sequencing and highlights their importance in uncovering CNV mutagenesis and pathogenesis in genomic disorders.

}, keywords = {Base Sequence, Comparative Genomic Hybridization, DNA Copy Number Variations, DNA Replication, Female, Gene Dosage, Gene Duplication, Gene Rearrangement, Genetic Association Studies, Genome, Human, Genomics, Humans, Male, Mutation, Pelizaeus-Merzbacher Disease, Sequence Analysis, DNA}, issn = {1460-2083}, doi = {10.1093/hmg/ddx102}, author = {Zhang, Ling and Wang, Jingmin and Zhang, Cheng and Li, Dongxiao and Carvalho, Claudia M B and Ji, Haoran and Xiao, Jianqiu and Wu, Ye and Zhou, Weichen and Wang, Hongyan and Jin, Li and Luo, Yang and Wu, Xiru and Lupski, James R and Zhang, Feng and Jiang, Yuwu} } @article {107, title = {Comparative Genomic Analyses of the Human NPHP1 Locus Reveal Complex Genomic Architecture and Its Regional Evolution in Primates.}, journal = {PLoS Genet}, volume = {11}, year = {2015}, month = {2015 Dec}, pages = {e1005686}, abstract = {

Many loci in the human genome harbor complex genomic structures that can result in susceptibility to genomic rearrangements leading to various genomic disorders. Nephronophthisis 1 (NPHP1, MIM$\#$ 256100) is an autosomal recessive disorder that can be caused by defects of NPHP1; the gene maps within the human 2q13 region where low copy repeats (LCRs) are abundant. Loss of function of NPHP1 is responsible for approximately 85\% of the NPHP1 cases-about 80\% of such individuals carry a large recurrent homozygous NPHP1 deletion that occurs via nonallelic homologous recombination (NAHR) between two flanking directly oriented ~45 kb LCRs. Published data revealed a non-pathogenic inversion polymorphism involving the NPHP1 gene flanked by two inverted ~358 kb LCRs. Using optical mapping and array-comparative genomic hybridization, we identified three potential novel structural variant (SV) haplotypes at the NPHP1 locus that may protect a haploid genome from the NPHP1 deletion. Inter-species comparative genomic analyses among primate genomes revealed massive genomic changes during evolution. The aggregated data suggest that dynamic genomic rearrangements occurred historically within the NPHP1 locus and generated SV haplotypes observed in the human population today, which may confer differential susceptibility to genomic instability and the NPHP1 deletion within a personal genome. Our study documents diverse SV haplotypes at a complex LCR-laden human genomic region. Comparative analyses provide a model for how this complex region arose during primate evolution, and studies among humans suggest that intra-species polymorphism may potentially modulate an individual{\textquoteright}s susceptibility to acquiring disease-associated alleles.

}, keywords = {Adaptor Proteins, Signal Transducing, Alleles, Animals, Comparative Genomic Hybridization, Evolution, Molecular, Gene Dosage, Gene Rearrangement, Genome, Human, Genomic Structural Variation, Haplotypes, Humans, Kidney Diseases, Cystic, Membrane Proteins, Primates}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005686}, author = {Yuan, Bo and Liu, Pengfei and Gupta, Aditya and Beck, Christine R and Tejomurtula, Anusha and Campbell, Ian M and Gambin, Tomasz and Simmons, Alexandra D and Withers, Marjorie A and Harris, R Alan and Rogers, Jeffrey and Schwartz, David C and Lupski, James R} } @article {346, title = {Complex genomic rearrangements at the PLP1 locus include triplication and quadruplication.}, journal = {PLoS Genet}, volume = {11}, year = {2015}, month = {2015 Mar}, pages = {e1005050}, abstract = {

Inverted repeats (IRs) can facilitate structural variation as crucibles of genomic rearrangement. Complex duplication-inverted triplication-duplication (DUP-TRP/INV-DUP) rearrangements that contain breakpoint junctions within IRs have been recently associated with both MECP2 duplication syndrome (MIM$\#$300260) and Pelizaeus-Merzbacher disease (PMD, MIM$\#$312080). We investigated 17 unrelated PMD subjects with copy number gains at the PLP1 locus including triplication and quadruplication of specific genomic intervals-16/17 were found to have a DUP-TRP/INV-DUP rearrangement product. An IR distal to PLP1 facilitates DUP-TRP/INV-DUP formation as well as an inversion structural variation found frequently amongst normal individuals. We show that a homology-or homeology-driven replicative mechanism of DNA repair can apparently mediate template switches within stretches of microhomology. Moreover, we provide evidence that quadruplication and potentially higher order amplification of a genomic interval can occur in a manner consistent with rolling circle amplification as predicted by the microhomology-mediated break induced replication (MMBIR) model.

}, keywords = {Chromosome Breakpoints, Chromosome Inversion, Gene Dosage, Gene Duplication, Humans, Myelin Proteolipid Protein, Pelizaeus-Merzbacher Disease}, issn = {1553-7404}, doi = {10.1371/journal.pgen.1005050}, author = {Beck, Christine R and Carvalho, Claudia M B and Banser, Linda and Gambin, Tomasz and Stubbolo, Danielle and Yuan, Bo and Sperle, Karen and McCahan, Suzanne M and Henneke, Marco and Seeman, Pavel and Garbern, James Y and Hobson, Grace M and Lupski, James R} } @article {109, title = {Mutations in Either TUBB or MAPRE2 Cause Circumferential Skin Creases Kunze Type.}, journal = {Am J Hum Genet}, volume = {97}, year = {2015}, month = {2015 Dec 03}, pages = {790-800}, abstract = {

Circumferential skin creases Kunze type (CSC-KT) is a specific congenital entity with an unknown genetic cause. The disease phenotype comprises characteristic circumferential skin creases accompanied by intellectual disability, a cleft palate, short stature, and dysmorphic features. Here, we report that mutations in either MAPRE2 or TUBB underlie the genetic origin of this syndrome. MAPRE2 encodes a member of the microtubule end-binding family of proteins that bind to the guanosine triphosphate cap at growing microtubule plus ends, and TUBB encodes a β-tubulin isotype that is expressed abundantly in the developing brain. Functional analyses of the TUBB mutants show multiple defects in the chaperone-dependent tubulin heterodimer folding and assembly pathway that leads to a compromised yield of native heterodimers. The TUBB mutations also have an impact on microtubule dynamics. For MAPRE2, we show that the mutations result in enhanced MAPRE2 binding to microtubules, implying an increased dwell time at microtubule plus ends. Further, in vivo analysis of MAPRE2 mutations in a zebrafish model of craniofacial development shows that the variants most likely perturb the patterning of branchial arches, either through excessive activity (under a recessive paradigm) or through haploinsufficiency (dominant de novo paradigm). Taken together, our data add CSC-KT to the growing list of tubulinopathies and highlight how multiple inheritance paradigms can affect dosage-sensitive biological systems so as to result in the same clinical defect.

}, keywords = {Adolescent, Animals, Brain, Child, Cutis Laxa, Female, Gene Dosage, Gene Expression Regulation, Developmental, Genes, Recessive, Hamartoma, Haploinsufficiency, Humans, Infant, Inheritance Patterns, Male, Microtubule-Associated Proteins, Microtubules, Mutation, Protein Folding, Protein Multimerization, Skin, Skin Abnormalities, Tubulin, Young Adult, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2015.10.014}, author = {Isrie, Mala and Breuss, Martin and Tian, Guoling and Hansen, Andi Harley and Cristofoli, Francesca and Morandell, Jasmin and Kupchinsky, Zachari A and Sifrim, Alejandro and Rodriguez-Rodriguez, Celia Maria and Dapena, Elena Porta and Doonanco, Kurston and Leonard, Norma and Tinsa, Faten and Moortgat, St{\'e}phanie and Ulucan, Hakan and Koparir, Erkan and Karaca, Ender and Katsanis, Nicholas and Marton, Valeria and Vermeesch, Joris Robert and Davis, Erica E and Cowan, Nicholas J and Keays, David Anthony and Van Esch, Hilde} } @article {175, title = {Structural variation mutagenesis of the human genome: Impact on disease and evolution.}, journal = {Environ Mol Mutagen}, volume = {56}, year = {2015}, month = {2015 06}, pages = {419-36}, abstract = {

Watson-Crick base-pair changes, or single-nucleotide variants (SNV), have long been known as a source of mutations. However, the extent to which DNA structural variation, including duplication and deletion copy number variants (CNV) and copy number neutral inversions and translocations, contribute to human genome variation and disease has been appreciated only recently. Moreover, the potential complexity of structural variants (SV) was not envisioned; thus, the frequency of complex genomic rearrangements and how such events form remained a mystery. The concept of genomic disorders, diseases due to genomic rearrangements and not sequence-based changes for which genomic architecture incite genomic instability, delineated a new category of conditions distinct from chromosomal syndromes and single-gene Mendelian diseases. Nevertheless, it is the mechanistic understanding of CNV/SV formation that has promoted further understanding of human biology and disease and provided insights into human genome and gene evolution. Environ. Mol. Mutagen. 56:419-436, 2015. {\textcopyright} 2015 Wiley Periodicals, Inc.

}, keywords = {Animals, Evolution, Molecular, Gene Dosage, Genetic Predisposition to Disease, Genome, Human, Genomic Structural Variation, Humans, Mutagenesis}, issn = {1098-2280}, doi = {10.1002/em.21943}, author = {Lupski, James R} } @article {209, title = {Dosage changes of a segment at 17p13.1 lead to intellectual disability and microcephaly as a result of complex genetic interaction of multiple genes.}, journal = {Am J Hum Genet}, volume = {95}, year = {2014}, month = {2014 Nov 06}, pages = {565-78}, abstract = {

The 17p13.1 microdeletion syndrome is a recently described genomic disorder with a core clinical phenotype of intellectual disability, poor to absent speech, dysmorphic features, and a constellation of more variable clinical features, most prominently microcephaly. We identified five subjects with copy-number variants (CNVs) on 17p13.1 for whom we performed detailed clinical and molecular studies. Breakpoint mapping and retrospective analysis of published cases refined the smallest region of overlap (SRO) for microcephaly to a genomic interval containing nine genes. Dissection of this phenotype in zebrafish embryos revealed a complex genetic architecture: dosage perturbation of four genes (ASGR1, ACADVL, DVL2, and GABARAP) impeded neurodevelopment and decreased dosage of the same loci caused a reduced mitotic index in~vitro. Moreover, epistatic analyses in~vivo showed that dosage perturbations of discrete gene pairings induce microcephaly. Taken together, these studies support a model in which concomitant dosage perturbation of multiple genes within the CNV drive the microcephaly and possibly other neurodevelopmental phenotypes associated with rearrangements in the 17p13.1 SRO.

}, keywords = {Abnormalities, Multiple, Acyl-CoA Dehydrogenase, Long-Chain, Adaptor Proteins, Signal Transducing, Animals, Asialoglycoprotein Receptor, Base Sequence, Cell Line, Chromosome Breakpoints, Chromosome Deletion, Chromosomes, Human, Pair 17, Dishevelled Proteins, Flow Cytometry, Gene Dosage, Humans, Immunohistochemistry, Intellectual Disability, Microcephaly, Microtubule-Associated Proteins, Molecular Sequence Data, Phosphoproteins, Retrospective Studies, Sequence Analysis, DNA, Smith-Magenis Syndrome, Syndrome, Zebrafish}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2014.10.006}, author = {Carvalho, Claudia M B and Vasanth, Shivakumar and Shinawi, Marwan and Russell, Chad and Ramocki, Melissa B and Brown, Chester W and Graakjaer, Jesper and Skytte, Anne-Bine and Vianna-Morgante, Angela M and Krepischi, Ana C V and Patel, Gayle S and Immken, LaDonna and Aleck, Kyrieckos and Lim, Cynthia and Cheung, Sau Wai and Rosenberg, Carla and Katsanis, Nicholas and Lupski, James R} } @article {255, title = {Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.}, journal = {Nat Genet}, volume = {46}, year = {2014}, month = {2014 Jun}, pages = {613-7}, abstract = {

Adrenal tumors autonomously producing cortisol cause Cushing{\textquoteright}s syndrome. We performed exome sequencing of 25 tumor-normal pairs and identified 2 subgroups. Eight tumors (including three carcinomas) had many somatic copy number variants (CNVs) with frequent deletion of CDC42 and CDKN2A, amplification of 5q31.2 and protein-altering mutations in TP53 and RB1. Seventeen tumors (all adenomas) had no somatic CNVs or TP53 or RB1 mutations. Six of these had known gain-of-function mutations in CTNNB1 (β-catenin) or GNAS (Gαs). Six others had somatic mutations in PRKACA (protein kinase A (PKA) catalytic subunit) resulting in a p.Leu206Arg substitution. Further sequencing identified this mutation in 13 of 63 tumors (35\% of adenomas with overt Cushing{\textquoteright}s syndrome). PRKACA, GNAS and CTNNB1 mutations were mutually exclusive. Leu206 directly interacts with the regulatory subunit of PKA, PRKAR1A. Leu206Arg PRKACA loses PRKAR1A binding, increasing the phosphorylation of downstream targets. PKA activity induces cortisol production and cell proliferation, providing a mechanism for tumor development. These findings define distinct mechanisms underlying adrenal cortisol-producing tumors.

}, keywords = {Adolescent, Adrenal Gland Neoplasms, Adult, Aged, Amino Acid Sequence, Base Sequence, cdc42 GTP-Binding Protein, Cell Proliferation, Cyclic AMP-Dependent Protein Kinase Catalytic Subunits, Cyclin-Dependent Kinase Inhibitor p16, DNA Copy Number Variations, Exome, Female, Gene Deletion, Gene Dosage, HEK293 Cells, Humans, Hydrocortisone, Male, Middle Aged, Molecular Sequence Data, Mutation, Phosphorylation, Sequence Analysis, DNA, Sequence Homology, Amino Acid}, issn = {1546-1718}, doi = {10.1038/ng.2956}, author = {Goh, Gerald and Scholl, Ute I and Healy, James M and Choi, Murim and Prasad, Manju L and Nelson-Williams, Carol and Kunstman, John W and Kuntsman, John W and Korah, Reju and Suttorp, Anna-Carinna and Dietrich, Dimo and Haase, Matthias and Willenberg, Holger S and St{\r a}lberg, Peter and Hellman, Per and Akerstr{\"o}m, G{\"o}ran and Bj{\"o}rklund, Peyman and Carling, Tobias and Lifton, Richard P} }