Prioritization of genes driving congenital phenotypes of patients with de novo genomic structural variants

BackgroundGenomic structural variants (SVs) can affect many genes and regulatory elements. Therefore, the molecular mechanisms driving the phenotypes of patients carrying de novo SVs are frequently unknown.MethodsWe applied a combination of systematic experimental and bioinformatic methods to improve the molecular diagnosis of 39 patients with multiple congenital abnormalities and/or intellectual disability harboring apparent de novo SVs, most with an inconclusive diagnosis after regular genetic testing.ResultsIn 7 of these cases (18%), whole-genome sequencing analysis revealed disease-relevant complexities of the SVs missed in routine microarray-based analyses. We developed a computational tool to predict the effects on genes directly affected by SVs and on genes indirectly affected likely due to the changes in chromatin organization and impact on regulatory mechanisms. By combining these functional predictions with extensive phenotype information, candidate driver genes were identified in 16/39 (41%) patients. In 8 cases, evidence was found for the involvement of multiple candidate drivers contributing to different parts of the phenotypes. Subsequently, we applied this computational method to two cohorts containing a total of 379 patients with previously detected and classified de novo SVs and identified candidate driver genes in 189 cases (50%), including 40 cases whose SVs were previously not classified as pathogenic. Pathogenic position effects were predicted in 28% of all studied cases with balanced SVs and in 11% of the cases with copy number variants.ConclusionsThese results demonstrate an integrated computational and experimental approach to predict driver genes based on analyses of WGS data with phenotype association and chromatin organization datasets. These analyses nominate new pathogenic loci and have strong potential to improve the molecular diagnosis of patients with de novo SVs.

[1]  Fowzan S Alkuraya,et al.  Computational Prediction of Position Effects of Apparently Balanced Human Chromosomal Rearrangements. , 2017, American journal of human genetics.

[2]  Mathieu Blanchette,et al.  A critical assessment of topologically associating domain prediction tools , 2017, Nucleic acids research.

[3]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[4]  D. Duboule,et al.  Impact of copy number variations (CNVs) on long-range gene regulation at the HoxD locus , 2012, Proceedings of the National Academy of Sciences.

[5]  H. Hakonarson,et al.  Monoallelic BMP2 Variants Predicted to Result in Haploinsufficiency Cause Craniofacial, Skeletal, and Cardiac Features Overlapping Those of 20p12 Deletions. , 2017, American Journal of Human Genetics.

[6]  J. Noonan,et al.  High-Resolution Epigenomic Atlas of Human Embryonic Craniofacial Development , 2018, Cell reports.

[7]  Anthony D. Schmitt,et al.  A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome. , 2016, Cell reports.

[8]  F. Quintero-Rivera,et al.  Familial Microdeletion of 17q24.3 Upstream of SOX9 Is Associated With Isolated Pierre Robin Sequence Due to Position Effect , 2013, American journal of medical genetics. Part A.

[9]  M. K. Rudd,et al.  Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. , 2015, American journal of human genetics.

[10]  Wendy K. Chung,et al.  De novo PHIP-predicted deleterious variants are associated with developmental delay, intellectual disability, obesity, and dysmorphic features , 2016, Cold Spring Harbor molecular case studies.

[11]  Jan O. Korbel,et al.  Phenotypic impact of genomic structural variation: insights from and for human disease , 2013, Nature Reviews Genetics.

[12]  Daning Lu,et al.  Chromosome conformation elucidates regulatory relationships in developing human brain , 2016, Nature.

[13]  Xiaoyu Chen,et al.  Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications , 2016, Bioinform..

[14]  O. Mäkitie,et al.  Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization , 2018, PLoS genetics.

[15]  Jonathan M. Cairns,et al.  Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters , 2016, Cell.

[16]  M. Terradas,et al.  Detection of Impaired DNA Replication and Repair in Micronuclei as Indicators of Genomic Instability and Chromothripsis. , 2018, Methods in molecular biology.

[17]  Mark Gerstein,et al.  Measuring the reproducibility and quality of Hi-C data , 2017, Genome Biology.

[18]  Wei Liu,et al.  Bottom-up precise synthesis of stable platinum dimers on graphene , 2017, Nature Communications.

[19]  Alexander Schönhuth,et al.  Characteristics of de novo structural changes in the human genome , 2015, Genome research.

[20]  J. Lupski,et al.  Mechanisms underlying structural variant formation in genomic disorders , 2016, Nature Reviews Genetics.

[21]  L. Coin,et al.  Genotype-free demultiplexing of pooled single-cell RNA-seq , 2019, Genome Biology.

[22]  A. Visel,et al.  Composition and dosage of a multipartite enhancer cluster control developmental expression of Indian hedgehog , 2017, Nature Genetics.

[23]  Tudor Groza,et al.  Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources , 2018, Nucleic Acids Res..

[24]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[25]  Gabor T. Marth,et al.  An integrated map of structural variation in 2,504 human genomes , 2015, Nature.

[26]  E. Birney,et al.  Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt , 2009, Nature Protocols.

[27]  P. Patel,et al.  X-linked congenital hypertrichosis syndrome is associated with interchromosomal insertions mediated by a human-specific palindrome near SOX3. , 2011, American journal of human genetics.

[28]  P. Eriksson,et al.  Notch, BMP and WNT/β-catenin network is impaired in endothelial cells of the patients with thoracic aortic aneurysm. , 2018, Atherosclerosis. Supplements.

[29]  Martin Vingron,et al.  Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis , 2018, Nature Genetics.

[30]  Michael Q. Zhang,et al.  Integrative analysis of 111 reference human epigenomes , 2015, Nature.

[31]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[32]  Jonathan M. Cairns,et al.  CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data , 2015, Genome Biology.

[33]  Leonardo Beccari,et al.  Large scale genomic reorganization of topological domains at the HoxD locus , 2017, Genome Biology.

[34]  Grace Tiao,et al.  An open resource of structural variation for medical and population genetics , 2019 .

[35]  J. Baptista,et al.  Modeling the Pathological Long-Range Regulatory Effects of Human Structural Variation with Patient-Specific hiPSCs. , 2019, Cell stem cell.

[36]  Haley J. Abel,et al.  SVScore: an impact prediction tool for structural variation , 2016, bioRxiv.

[37]  D. Goldstein,et al.  Genic Intolerance to Functional Variation and the Interpretation of Personal Genomes , 2013, PLoS genetics.

[38]  Peter Langfelder,et al.  Is human blood a good surrogate for brain tissue in transcriptional studies? , 2010, BMC Genomics.

[39]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[40]  B. Nowakowska,et al.  Clinical interpretation of copy number variants in the human genome , 2017, Journal of Applied Genetics.

[41]  Lilia M. Iakoucheva,et al.  Paternally inherited cis-regulatory structural variants are associated with autism , 2018, Science.

[42]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[43]  A. Munnich,et al.  Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence , 2009, Nature Genetics.

[44]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[45]  Stephen J Glatt,et al.  On the outside, looking in: A review and evaluation of the comparability of blood and brain “‐omes” , 2013, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[46]  Donna M. Muzny,et al.  Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation , 2017, The New England journal of medicine.

[47]  F. Cunningham,et al.  The Ensembl Variant Effect Predictor , 2016, Genome Biology.

[48]  Laura E. DeMare,et al.  The Evolution of Lineage-Specific Regulatory Activities in the Human Embryonic Limb , 2013, Cell.

[49]  Manuel Corpas,et al.  DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. , 2009, American journal of human genetics.

[50]  Chung K. Chang,et al.  The 5p15.33 Locus Is Associated with Risk of Lung Adenocarcinoma in Never-Smoking Females in Asia , 2010, PLoS genetics.

[51]  L. Vissers,et al.  Genome sequencing identifies major causes of severe intellectual disability , 2014, Nature.

[52]  M. Swertz,et al.  The phenotypic spectrum of proximal 6q deletions based on a large cohort derived from social media and literature reports , 2018, European Journal of Human Genetics.

[53]  Prashant S. Emani,et al.  Comprehensive functional genomic resource and integrative model for the human brain , 2018, Science.

[54]  Chang Liu,et al.  Altered chromatin compaction and histone methylation drive non-additive gene expression in an interspecific Arabidopsis hybrid , 2017, Genome Biology.

[55]  N. Tommerup,et al.  Regulatory variants of FOXG1 in the context of its topological domain organisation , 2018, European Journal of Human Genetics.

[56]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[57]  S. Mundlos,et al.  Structural variation in the 3D genome , 2018, Nature Reviews Genetics.

[58]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[59]  A. Visel,et al.  Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions , 2015, Cell.

[60]  W. Kühlbrandt,et al.  Structure and in situ organisation of the Pyrococcus furiosus archaellum machinery , 2017, eLife.

[61]  R. Siebert,et al.  Genotype–phenotype correlation in eight new patients with a deletion encompassing 2q31.1 , 2010, American journal of medical genetics. Part A.

[62]  S. Sati,et al.  Looking for Broken TAD Boundaries and Changes on DNA Interactions: Clinical Guide to 3D Chromatin Change Analysis in Complex Chromosomal Rearrangements and Chromothripsis. , 2018, Methods in molecular biology.

[63]  D. Duboule,et al.  A Switch Between Topological Domains Underlies HoxD Genes Collinearity in Mouse Limbs , 2013, Science.

[64]  V. Jobanputra,et al.  Position effect on FGF13 associated with X-linked congenital generalized hypertrichosis , 2013, Proceedings of the National Academy of Sciences.

[65]  S. Lewis,et al.  Deletions of chromosomal regulatory boundaries are associated with congenital disease , 2014, Genome Biology.

[66]  G. Ciriello,et al.  Comparison of computational methods for the identification of topologically associating domains , 2018, Genome Biology.

[67]  Ryan L. Collins,et al.  Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation. , 2015, American journal of human genetics.

[68]  Jing Liang,et al.  Chromatin architecture reorganization during stem cell differentiation , 2015, Nature.

[69]  Edwin Cuppen,et al.  Sambamba: fast processing of NGS alignment formats , 2015, Bioinform..

[70]  Giacomo Cavalli,et al.  Organization and function of the 3D genome , 2016, Nature Reviews Genetics.

[71]  Edwin Cuppen,et al.  Mapping and phasing of structural variation in patient genomes using nanopore sequencing , 2017, Nature Communications.

[72]  Shuwen Huang,et al.  X-Linked Dominant Congenital Ptosis Cosegregating with an Interstitial Insertion of a Chromosome 1p21.3 Fragment into a Quasipalindromic Sequence in Xq27.1 , 2014 .

[73]  S. South,et al.  Detection of a de novo interstitial 2q microdeletion by CGH microarray analysis in a patient with limb malformations, microcephaly and mental retardation , 2007, American journal of medical genetics. Part A.

[74]  Tudor Groza,et al.  The Human Phenotype Ontology in 2017 , 2016, Nucleic Acids Res..

[75]  Marcel H. Schulz,et al.  Clinical diagnostics in human genetics with semantic similarity searches in ontologies. , 2009, American journal of human genetics.

[76]  Thomas Zichner,et al.  DELLY: structural variant discovery by integrated paired-end and split-read analysis , 2012, Bioinform..

[77]  James Y. Zou.  Analysis of protein-coding genetic variation in 60,706 humans , 2015, Nature.

[78]  S. Zuchner,et al.  Whole Genome Sequencing Identifies a 78 kb Insertion from Chromosome 8 as the Cause of Charcot-Marie-Tooth Neuropathy CMTX3 , 2016, PLoS genetics.

[79]  Jonathan M. Cairns,et al.  Global reorganisation of cis-regulatory units upon lineage commitment of human embryonic stem cells , 2017, eLife.

[80]  James N. Hughes,et al.  Interchromosomal insertional translocation at Xq26.3 alters SOX3 expression in an individual with XX male sex reversal. , 2015, The Journal of clinical endocrinology and metabolism.

[81]  S. Mundlos,et al.  Formation of new chromatin domains determines pathogenicity of genomic duplications , 2016, Nature.

[82]  Michael Brudno,et al.  Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine , 2016, npj Genomic Medicine.

[83]  J. R. MacDonald,et al.  A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data. , 2018, American journal of human genetics.

[84]  Peter H. L. Krijger,et al.  Regulation of disease-associated gene expression in the 3D genome , 2016, Nature Reviews Molecular Cell Biology.

[85]  Leonardo Beccari,et al.  The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes , 2017, bioRxiv.

[86]  L. Mirny,et al.  Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data , 2013, Nature Reviews Genetics.

[87]  C. Tyler-Smith,et al.  Ancient DNA and the rewriting of human history: be sparing with Occam’s razor , 2016, Genome Biology.

[88]  Yan Mei,et al.  The RNA-binding protein hnRNPLL induces a T cell alternative splicing program delineated by differential intron retention in polyadenylated RNA , 2014, Genome Biology.

[89]  R. Pfundt,et al.  Pathogenic or not? Assessing the clinical relevance of copy number variants , 2013, Clinical genetics.

[90]  Insuk Lee,et al.  Characterising and Predicting Haploinsufficiency in the Human Genome , 2010, PLoS genetics.

[91]  David R. FitzPatrick,et al.  Paediatric genomics: diagnosing rare disease in children , 2018, Nature Reviews Genetics.

[92]  Edwin Cuppen,et al.  The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies , 2016, Nature Genetics.

[93]  Daniel S. Kim,et al.  Lineage-specific dynamic and pre-established enhancer–promoter contacts cooperate in terminal differentiation , 2017, Nature Genetics.