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Niu Y, Fan X, Yang Y, Li J, Lian J, Wang L, Zhang Y, Tang Y, Tang Z. Haplotype-resolved assembly of a pig genome using single-sperm sequencing. Commun Biol 2024; 7:738. [PMID: 38890535 PMCID: PMC11189477 DOI: 10.1038/s42003-024-06397-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 05/29/2024] [Indexed: 06/20/2024] Open
Abstract
Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers. The chromosome-level phased assembly showed higher phasing accuracy than methods that rely only on HiFi reads. The use of single-sperm sequencing data enabled the construction of a genetic map, successfully mapping the sperm motility trait to a specific region on chromosome 1 (105.40-110.70 Mb). Furthermore, with the assistance of Y chromosome-bearing sperm data, 26.16 Mb Y chromosome sequences were assembled. We report a reliable approach for assembling chromosome-level phased genomes and reveal the potential of sperm population in basic biology research and sperm phenotype research.
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Affiliation(s)
- Yongchao Niu
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xinhao Fan
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yalan Yang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Jiang Li
- Biozeron Shenzhen, Inc., Shenzhen, China
| | | | - Liu Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China
| | - Yongjin Zhang
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China
| | - Yijie Tang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhonglin Tang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Foshan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agriculture Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
- GuangXi Engineering Centre for Resource Development of Bama Xiang Pig, Bama, China.
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
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Chan AP, Choi Y, Rangan A, Zhang G, Podder A, Berens M, Sharma S, Pirrotte P, Byron S, Duggan D, Schork NJ. Interrogating the Human Diplome: Computational Methods, Emerging Applications, and Challenges. Methods Mol Biol 2023; 2590:1-30. [PMID: 36335489 DOI: 10.1007/978-1-0716-2819-5_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Human DNA sequencing protocols have revolutionized human biology, biomedical science, and clinical practice, but still have very important limitations. One limitation is that most protocols do not separate or assemble (i.e., "phase") the nucleotide content of each of the maternally and paternally derived chromosomal homologs making up the 22 autosomal pairs and the chromosomal pair making up the pseudo-autosomal region of the sex chromosomes. This has led to a dearth of studies and a consequent underappreciation of many phenomena of fundamental importance to basic and clinical genomic science. We discuss a few protocols for obtaining phase information as well as their limitations, including those that could be used in tumor phasing settings. We then describe a number of biological and clinical phenomena that require phase information. These include phenomena that require precise knowledge of the nucleotide sequence in a chromosomal segment from germline or somatic cells, such as DNA binding events, and insight into unique cis vs. trans-acting functionally impactful variant combinations-for example, variants implicated in a phenotype governed by compound heterozygosity. In addition, we also comment on the need for reliable and consensus-based diploid-context computational workflows for variant identification as well as the need for laboratory-based functional verification strategies for validating cis vs. trans effects of variant combinations. We also briefly describe available resources, example studies, as well as areas of further research, and ultimately argue that the science behind the study of human diploidy, referred to as "diplomics," which will be enabled by nucleotide-level resolution of phased genomes, is a logical next step in the analysis of human genome biology.
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Affiliation(s)
- Agnes P Chan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Yongwook Choi
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Aditya Rangan
- Courant Institute of Mathematical Sciences at New York University, New York, NY, USA
| | - Guangfa Zhang
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Avijit Podder
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
| | - Michael Berens
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sunil Sharma
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Patrick Pirrotte
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Sara Byron
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Dave Duggan
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA
- The City of Hope National Medical Center, Duarte, CA, USA
| | - Nicholas J Schork
- The Translational Genomics Research Institute (TGen), part of the City of Hope National Medical Center, Phoenix, AZ, USA.
- The City of Hope National Medical Center, Duarte, CA, USA.
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3
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Hoehe MR, Herwig R. Analysis of 1276 Haplotype-Resolved Genomes Allows Characterization of Cis- and Trans-Abundant Genes. Methods Mol Biol 2023; 2590:237-272. [PMID: 36335503 DOI: 10.1007/978-1-0716-2819-5_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Many methods for haplotyping have materialized, but their application on a significant scale has been rare to date. Here we summarize analyses that were carried out in 1092 genomes from the 1000 Genomes Consortium and validated in an unprecedented number of 184 PGP genomes that have been experimentally haplotype-resolved by application of the Long-Fragment Read (LFR) technology. These analyses provided first insights into the diplotypic nature of human genomes and its potential functional implications. Thus, protein-changing variants were not randomly distributed between the two homologues of 18,121 autosomal protein-coding genes but occurred significantly more frequently in cis than in trans configurations in virtually each of the 1276 phased genomes. This resulted in global cis/trans ratios of ~60:40, establishing "cis abundance" as a universal characteristic of diploid human genomes. This phenomenon was based on two different classes of genes, a larger one exhibiting cis configurations of protein-changing variants in excess, so-called "cis-abundant" genes, and a smaller one of "trans-abundant" genes. These two gene classes, which together constitute a common diplotypic exome, were further functionally distinguished by means of gene ontology (GO) and pathway enrichment analysis. Moreover, they were distinguishable in terms of their effects on the human interactome, where they constitute distinct cis and trans modules, as shown with network propagation on a large integrated protein-protein interaction network. These analyses, recently performed with updated database and analysis tools, further consolidated the characterization of cis- and trans-abundant genes while expanding previous results. In this chapter, we present the key results along with the materials and methods to motivate readers to investigate these findings independently and gain further insights into the diplotypic nature of genes and genomes.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany.
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
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4
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Direct Chromosomal Phasing: An Easy and Fast Approach for Broadening Prenatal Diagnostic Applicability. THALASSEMIA REPORTS 2022. [DOI: 10.3390/thalassrep12030011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The assignment of alleles to haplotypes in prenatal diagnostic assays has traditionally depended on family study analyses. However, this prevents the wide application of prenatal diagnosis based on haplotype analysis, especially in countries with dispersed populations. Here, we present an easy and fast approach using Droplet Digital PCR for the direct determination of haplotype blocks, overcoming the necessity for acquiring other family members’ genetic samples. We demonstrate this approach on nine families that were referred to our center for a prenatal diagnosis of β-thalassaemia using four highly polymorphic single nucleotide variations and the most common pathogenic β-thalassaemia variation in our population. Our approach resulted in the successful direct chromosomal phasing and haplotyping for all nine of the families analyzed, demonstrating a complete agreement with the haplotypes that are ascertained based on family trios. The clinical utility of this approach is envisaged to open the application of prenatal diagnosis for β-thalassaemia to all cases, while simultaneously providing a model for extending the prenatal diagnostic application of other monogenic diseases as well.
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Farrer RA. HaplotypeTools: a toolkit for accurately identifying recombination and recombinant genotypes. BMC Bioinformatics 2021; 22:560. [PMID: 34809571 PMCID: PMC8607637 DOI: 10.1186/s12859-021-04473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background Identifying haplotypes is central to sequence analysis in diploid or polyploid genomes. Despite this, there remains a lack of research and tools designed for physical phasing and its downstream analysis. Results HaplotypeTools is a new toolset to phase variant sites using VCF and BAM files and to analyse phased VCFs. Phasing is achieved via the identification of reads overlapping ≥ 2 heterozygous positions and then extended by additional reads, a process that can be parallelized across a computer cluster. HaplotypeTools includes various utility scripts for downstream analysis including crossover detection and phylogenetic placement of haplotypes to other lineages or species. HaplotypeTools was assessed for accuracy against WhatsHap using simulated short and long reads, demonstrating higher accuracy, albeit with reduced haplotype length. HaplotypeTools was also tested on real Illumina data to determine the ancestry of hybrid fungal isolate Batrachochytrium dendrobatidis (Bd) SA-EC3, finding 80% of haplotypes across the genome phylogenetically cluster with parental lineages BdGPL (39%) and BdCAPE (41%), indicating those are the parental lineages. Finally, ~ 99% of phasing was conserved between overlapping phase groups between SA-EC3 and either parental lineage, indicating mitotic gene conversion/parasexuality as the mechanism of recombination for this hybrid isolate. HaplotypeTools is open source and freely available from https://github.com/rhysf/HaplotypeTools under the MIT License. Conclusions HaplotypeTools is a powerful resource for analyzing hybrid or recombinant diploid or polyploid genomes and identifying parental ancestry for sub-genomic regions.
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Affiliation(s)
- Rhys A Farrer
- Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter, UK.
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6
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Garg S. Computational methods for chromosome-scale haplotype reconstruction. Genome Biol 2021; 22:101. [PMID: 33845884 PMCID: PMC8040228 DOI: 10.1186/s13059-021-02328-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
High-quality chromosome-scale haplotype sequences of diploid genomes, polyploid genomes, and metagenomes provide important insights into genetic variation associated with disease and biodiversity. However, whole-genome short read sequencing does not yield haplotype information spanning whole chromosomes directly. Computational assembly of shorter haplotype fragments is required for haplotype reconstruction, which can be challenging owing to limited fragment lengths and high haplotype and repeat variability across genomes. Recent advancements in long-read and chromosome-scale sequencing technologies, alongside computational innovations, are improving the reconstruction of haplotypes at the level of whole chromosomes. Here, we review recent and discuss methodological progress and perspectives in these areas.
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Affiliation(s)
- Shilpa Garg
- Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Lee Yu HL, Fan TW, Hsing IM. Oligonucleotide hybridization with magnetic separation assay for multiple SNP phasing. Anal Chim Acta X 2020; 5:100050. [PMID: 33117988 PMCID: PMC7587028 DOI: 10.1016/j.acax.2020.100050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 10/29/2022] Open
Abstract
Since humans have two copies of each gene, multiple mutations in different loci may or may not be found on the same strand of DNA (i.e., inherited from one parent). When a person is heterozygous at more than one position, the placement of these mutations, also called the haplotype phase, (i.e., cis for the same strand and trans for different strands) can result in the expression of different amount and type of proteins. In this work, we described an enzyme-free method to phase two single nucleotide polymorphisms (SNPs) using two fluorophore/quencher-labelled probes, where one of which was biotinylated. The fluorescence signal was obtained twice: first, after the addition of the labelled probes and second, after the addition of the magnetic beads. The first signal was shown to be proportional to the total number of SNP A and SNP B present in the target analyte, while the second signal showed a marked decrease of the fluorescence signal from the non-biotinylated probe when the SNPs were in trans, showing that the probe immobilized on the magnetic bead selectively captures targets with SNPs in a cis configuration. We then mimic the nature of the human genome which consists of two haplotype copies of each gene, and showed that 250 nM of the 10 possible pairs of haplotypes could be differentiated using a combination of fluorescence microscopy and fluorescence detection.
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Affiliation(s)
- Henson L. Lee Yu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Tsz Wing Fan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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8
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Qi R, Luo Y, Zhang L, Weng Y, Surento W, Jahanshad N, Xu Q, Yin Y, Li L, Cao Z, Thompson PM, Lu GM. FKBP5 haplotypes and PTSD modulate the resting-state brain activity in Han Chinese adults who lost their only child. Transl Psychiatry 2020; 10:91. [PMID: 32170058 PMCID: PMC7070023 DOI: 10.1038/s41398-020-0770-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/19/2020] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
The stress-related gene FKBP5 has been related to dysregulated glucocorticoid receptor (GR) signaling, showing increased GR sensitivity in trauma-exposed subjects with post-traumatic stress disorder (PTSD) but not in those without PTSD. However, the neural mechanism underlying the effects of FKBP5 remains poorly understood. Two hundred and thirty-seven Han Chinese adults who had lost their only child were included. Four FKBP5 single nucleotide polymorphisms (rs3800373, rs9296158, rs1360780, and rs9470080) were genotyped. All 179 participants were successfully divided into three FKBP5 diplotype subgroups according to two major FKBP5 H1 and H2 yin yang haplotypes. Brain average spectral power was compared using a two-way (PTSD diagnosis and FKBP5 diplotypes) analysis of covariance within four separate frequency bands (slow-5, slow-4, slow-3, and slow-2). Adults with PTSD showed lower spectral power in bilateral parietal lobules in slow-4 and in left inferior frontal gyrus (IFG) in slow-5. There was significant FKBP5 diplotype main effect in anterior cingulate cortex (ACC) in slow-4 (H1/H1 higher than other two subgroups), and in precentral/postcentral gyri and middle cingulate cortex (MCC) in slow-3 (H2/H2 higher than other two subgroups). Also, there was a significant diagnosis × FKBP5 diplotype interaction effect in right parietal lobule in slow-3. These findings suggest that adults with PTSD have lower low-frequency power in executive control network regions. Lower power in ACC and greater power in the motor/sensory areas in FKBP5 high-risk diplotype group suggest a disturbance of emotional processing and hypervigilance/sensitization to threatening stimuli. The interaction effect of diagnosis × FKBP5 in parietal lobule may contribute to PTSD development.
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Affiliation(s)
- Rongfeng Qi
- grid.41156.370000 0001 2314 964XDepartment of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, 210002 Nanjing, Jiangsu China ,grid.42505.360000 0001 2156 6853Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA 90292 USA
| | - Yifeng Luo
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, 75 Tongzhenguan Road, 214200 Wuxi, China
| | - Li Zhang
- grid.216417.70000 0001 0379 7164Mental Health Institute of the Second Xiangya Hospital, Central South University, China National Clinical Research Center for Mental Health Disorders, National Technology Institute of Psychiatry, 139 Middle Renmin Road, 410011 Changsha, Hunan China
| | - Yifei Weng
- grid.41156.370000 0001 2314 964XDepartment of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, 210002 Nanjing, Jiangsu China
| | - Wesley Surento
- grid.42505.360000 0001 2156 6853Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA 90292 USA
| | - Neda Jahanshad
- grid.42505.360000 0001 2156 6853Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA 90292 USA
| | - Qiang Xu
- grid.41156.370000 0001 2314 964XDepartment of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, 210002 Nanjing, Jiangsu China
| | - Yan Yin
- Psychology Department, Hangzhou Seventh People’s Hospital, 310013 Hangzhou, Zhejiang China
| | - Lingjiang Li
- grid.216417.70000 0001 0379 7164Mental Health Institute of the Second Xiangya Hospital, Central South University, China National Clinical Research Center for Mental Health Disorders, National Technology Institute of Psychiatry, 139 Middle Renmin Road, 410011 Changsha, Hunan China
| | - Zhihong Cao
- Department of Radiology, The Affiliated Yixing Hospital of Jiangsu University, 75 Tongzhenguan Road, 214200 Wuxi, China
| | - Paul M. Thompson
- grid.42505.360000 0001 2156 6853Imaging Genetics Center, Mark and Mary Stevens Neuroimaging and Informatics Institute, University of Southern California, Marina del Rey, CA 90292 USA
| | - Guang Ming Lu
- Department of Medical Imaging, Jinling Hospital, Medical School of Nanjing University, 210002, Nanjing, Jiangsu, China.
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9
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Shi D, Wu J, Tang H, Yin H, Wang H, Wang R, Wang R, Qian M, Wu J, Qi K, Xie Z, Wang Z, Zhao X, Zhang S. Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants. Genome Res 2019; 29:1889-1899. [PMID: 31649061 PMCID: PMC6836740 DOI: 10.1101/gr.251033.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 10/01/2019] [Indexed: 11/30/2022]
Abstract
Genome assemblies from diploid organisms create mosaic sequences alternating between parental alleles, which can create erroneous gene models and other problems. In animals, a popular strategy to generate haploid genome-resolved assemblies has been the sampling of (haploid) gametes, and the advent of single-cell sequencing has further advanced such methods. However, several challenges for the isolation and amplification of DNA from plant gametes have limited such approaches in plants. Here, we combined a new approach for pollen protoplast isolation with a single-cell DNA amplification technique and then used a “barcoding” bioinformatics strategy to incorporate haploid-specific sequence data from 12 pollen cells, ultimately enabling the efficient and accurate phasing of the pear genome into its A and B haploid genomes. Beyond revealing that 8.12% of the genes in the pear reference genome feature mosaic assemblies and enabling a previously impossible analysis of allelic affects in pear gene expression, our new haploid genome assemblies provide high-resolution information about recombination during meiosis in pollen. Considering that outcrossing pear is an angiosperm species featuring very high heterozygosity, our method for rapidly phasing genome assemblies is potentially applicable to several yet-unsequenced outcrossing angiosperm species in nature.
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Affiliation(s)
- Dongqing Shi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Jun Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian Province, China
| | - Hao Yin
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Hongtao Wang
- School of Life Science, Henan University, Kaifeng 475004, China
| | - Ran Wang
- College of Agriculture, Qingdao Agricultural University, Qingdao 266109, China
| | - Runze Wang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Qian
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Juyou Wu
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Kaijie Qi
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhihua Xie
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | | | | | - Shaoling Zhang
- Centre of Pear Engineering Technology Research, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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10
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Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
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Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
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11
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Neale SA, Kambara K, Salt TE, Bertrand D. Receptor variants and the development of centrally acting medications. DIALOGUES IN CLINICAL NEUROSCIENCE 2019. [PMID: 31636489 PMCID: PMC6787545 DOI: 10.31887/dcns.2019.21.2/dbertrand] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The progressive changes in research paradigms observed in the largest
pharmaceutical companies and the burgeoning of biotechnology startups over the
last 10 years have generated a need for outsourcing research facilities. In
parallel, progress made in the fields of genomics, protein expression in
recombinant systems, and electrophysiological recording methods have offered new
possibilities for the development of contract research organizations (CROs).
Successful partnering between pharmaceutical companies and CROs largely depends
upon the competences and scientific quality on offer for the discovery of novel
active molecules and targets. Thus, it is critical to review the knowledge in
the field of neuroscience research, how genetic approaches are augmenting our
knowledge, and how they can be applied in the translation from the
identification of potential molecules up to the first clinical trials. Taking
these together, it is apparent that CROs have an important role to play in the
neuroscience of drug discovery.
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Affiliation(s)
- Stuart A Neale
- Neurexpert Limited, The Core, Science Central, Newcastle Upon Tyne, UK
| | | | - Thomas E Salt
- Neurexpert Limited, The Core, Science Central, Newcastle Upon Tyne, UK; Honorary Professor, University of Newcastle, Newcastle, UK
| | - Daniel Bertrand
- HiQScreen Sàrl, Geneva, Switzerland; Emeritus Professor, Medical Faculty, Geneva, Switzerland
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12
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Latif WA, Ggha S. Understanding Neurobehavioural Dynamics: A Close-Up View on Psychiatry and Quantum Mechanics. Malays J Med Sci 2019; 26:147-156. [PMID: 30914902 PMCID: PMC6419875 DOI: 10.21315/mjms2019.26.1.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 08/27/2018] [Indexed: 12/01/2022] Open
Abstract
Psychiatric disorders are prevalent throughout the world and causes heavy burden on mankind. Alone in US, billions of dollars are used for treatment purposes annually. Although advances in treatment strategies had witnessed recently, however the efficacy and overall outcome weren’t quite promising. In neurobehavioural sciences, old problems survive through ages and with psychiatric disease, the phenomenon turns intensely complex. While our understanding of brain is mostly based on concepts of particle physics, its functions largely follow the principles of quantum mechanics. The current therapeutics relies on understanding of brain as a material entity that turns to be one of the chief reasons for the unsatisfactory therapeutic outcomes. Collectively, as mankind we are suffering huge loss due to the least effective treatment strategies. Even though we just begin to understand about how brain works, we also do not know much about quantum mechanics and how subatomic particles behave with quantum properties. Though it is apparent that quantum properties like particle and wave function duality coincides with the fundamental aspects of brain and mind duality, thus must share some common basis. Here in this article, an opinion is set that quantum mechanics in association with brain and more specifically psychiatry may take us towards a better understanding about brain, behaviour and how we approach towards treatment.
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Affiliation(s)
- Wani Ab Latif
- Cytogenetics and Molecular Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Science, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
| | - Shadab Ggha
- Cytogenetics and Molecular Toxicology Laboratory, Section of Genetics, Department of Zoology, Faculty of Life Science, Aligarh Muslim University, Aligarh, 202002, Uttar Pradesh, India
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13
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Spooner W, McLaren W, Slidel T, Finch DK, Butler R, Campbell J, Eghobamien L, Rider D, Kiefer CM, Robinson MJ, Hardman C, Cunningham F, Vaughan T, Flicek P, Huntington CC. Haplosaurus computes protein haplotypes for use in precision drug design. Nat Commun 2018; 9:4128. [PMID: 30297836 PMCID: PMC6175845 DOI: 10.1038/s41467-018-06542-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 09/07/2018] [Indexed: 01/08/2023] Open
Abstract
Selecting the most appropriate protein sequences is critical for precision drug design. Here we describe Haplosaurus, a bioinformatic tool for computation of protein haplotypes. Haplosaurus computes protein haplotypes from pre-existing chromosomally-phased genomic variation data. Integration into the Ensembl resource provides rapid and detailed protein haplotypes retrieval. Using Haplosaurus, we build a database of unique protein haplotypes from the 1000 Genomes dataset reflecting real-world protein sequence variability and their prevalence. For one in seven genes, their most common protein haplotype differs from the reference sequence and a similar number differs on their most common haplotype between human populations. Three case studies show how knowledge of the range of commonly encountered protein forms predicted in populations leads to insights into therapeutic efficacy. Haplosaurus and its associated database is expected to find broad applications in many disciplines using protein sequences and particularly impactful for therapeutics design.
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Affiliation(s)
- William Spooner
- Eagle Genomics Ltd., Biodata Innovation Centre, Wellcome Genome Campus, Hinxton, Cambridge, CB10 3DR UK
- Genomics England, QMUL Dawson Hall, London, EC1M 6BQ UK
| | - William McLaren
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | | | - Robin Butler
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | - David Rider
- MedImmune Ltd., Granta Park, Cambridge, CB21 4QR UK
| | | | | | | | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | | | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD UK
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14
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Choi Y, Chan AP, Kirkness E, Telenti A, Schork NJ. Comparison of phasing strategies for whole human genomes. PLoS Genet 2018; 14:e1007308. [PMID: 29621242 PMCID: PMC5903673 DOI: 10.1371/journal.pgen.1007308] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 04/17/2018] [Accepted: 03/13/2018] [Indexed: 12/17/2022] Open
Abstract
Humans are a diploid species that inherit one set of chromosomes paternally and one homologous set of chromosomes maternally. Unfortunately, most human sequencing initiatives ignore this fact in that they do not directly delineate the nucleotide content of the maternal and paternal copies of the 23 chromosomes individuals possess (i.e., they do not 'phase' the genome) often because of the costs and complexities of doing so. We compared 11 different widely-used approaches to phasing human genomes using the publicly available 'Genome-In-A-Bottle' (GIAB) phased version of the NA12878 genome as a gold standard. The phasing strategies we compared included laboratory-based assays that prepare DNA in unique ways to facilitate phasing as well as purely computational approaches that seek to reconstruct phase information from general sequencing reads and constructs or population-level haplotype frequency information obtained through a reference panel of haplotypes. To assess the performance of the 11 approaches, we used metrics that included, among others, switch error rates, haplotype block lengths, the proportion of fully phase-resolved genes, phasing accuracy and yield between pairs of SNVs. Our comparisons suggest that a hybrid or combined approach that leverages: 1. population-based phasing using the SHAPEIT software suite, 2. either genome-wide sequencing read data or parental genotypes, and 3. a large reference panel of variant and haplotype frequencies, provides a fast and efficient way to produce highly accurate phase-resolved individual human genomes. We found that for population-based approaches, phasing performance is enhanced with the addition of genome-wide read data; e.g., whole genome shotgun and/or RNA sequencing reads. Further, we found that the inclusion of parental genotype data within a population-based phasing strategy can provide as much as a ten-fold reduction in phasing errors. We also considered a majority voting scheme for the construction of a consensus haplotype combining multiple predictions for enhanced performance and site coverage. Finally, we also identified DNA sequence signatures associated with the genomic regions harboring phasing switch errors, which included regions of low polymorphism or SNV density.
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Affiliation(s)
- Yongwook Choi
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Agnes P. Chan
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ewen Kirkness
- Human Longevity, Inc., San Diego, California, United States of America
| | - Amalio Telenti
- J. Craig Venter Institute, La Jolla, California, United States of America
| | - Nicholas J. Schork
- J. Craig Venter Institute, La Jolla, California, United States of America
- University of California San Diego, La Jolla, California, United States of America
- The Translational Genomics Research Institute (TGen), Phoenix, Arizona, United States of America
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15
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Fan TW, Yu HLL, Hsing IM. Conditional Displacement Hybridization Assay for Multiple SNP Phasing. Anal Chem 2017; 89:9961-9966. [DOI: 10.1021/acs.analchem.7b02300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tsz Wing Fan
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henson L. Lee Yu
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - I-Ming Hsing
- Department
of Chemical and Biomolecular Engineering and ‡Division of Biomedical Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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16
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Maretty L, Jensen JM, Petersen B, Sibbesen JA, Liu S, Villesen P, Skov L, Belling K, Theil Have C, Izarzugaza JMG, Grosjean M, Bork-Jensen J, Grove J, Als TD, Huang S, Chang Y, Xu R, Ye W, Rao J, Guo X, Sun J, Cao H, Ye C, van Beusekom J, Espeseth T, Flindt E, Friborg RM, Halager AE, Le Hellard S, Hultman CM, Lescai F, Li S, Lund O, Løngren P, Mailund T, Matey-Hernandez ML, Mors O, Pedersen CNS, Sicheritz-Pontén T, Sullivan P, Syed A, Westergaard D, Yadav R, Li N, Xu X, Hansen T, Krogh A, Bolund L, Sørensen TIA, Pedersen O, Gupta R, Rasmussen S, Besenbacher S, Børglum AD, Wang J, Eiberg H, Kristiansen K, Brunak S, Schierup MH. Sequencing and de novo assembly of 150 genomes from Denmark as a population reference. Nature 2017; 548:87-91. [PMID: 28746312 DOI: 10.1038/nature23264] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 06/04/2017] [Indexed: 12/17/2022]
Abstract
Hundreds of thousands of human genomes are now being sequenced to characterize genetic variation and use this information to augment association mapping studies of complex disorders and other phenotypic traits. Genetic variation is identified mainly by mapping short reads to the reference genome or by performing local assembly. However, these approaches are biased against discovery of structural variants and variation in the more complex parts of the genome. Hence, large-scale de novo assembly is needed. Here we show that it is possible to construct excellent de novo assemblies from high-coverage sequencing with mate-pair libraries extending up to 20 kilobases. We report de novo assemblies of 150 individuals (50 trios) from the GenomeDenmark project. The quality of these assemblies is similar to those obtained using the more expensive long-read technology. We use the assemblies to identify a rich set of structural variants including many novel insertions and demonstrate how this variant catalogue enables further deciphering of known association mapping signals. We leverage the assemblies to provide 100 completely resolved major histocompatibility complex haplotypes and to resolve major parts of the Y chromosome. Our study provides a regional reference genome that we expect will improve the power of future association mapping studies and hence pave the way for precision medicine initiatives, which now are being launched in many countries including Denmark.
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Affiliation(s)
- Lasse Maretty
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jacob Malte Jensen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Bent Petersen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jonas Andreas Sibbesen
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Siyang Liu
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.,BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Palle Villesen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Kirstine Belling
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Christian Theil Have
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jose M G Izarzugaza
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Marie Grosjean
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jakob Grove
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Thomas D Als
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shujia Huang
- BGI-Shenzhen, Shenzhen 518083, China.,School of Bioscience and Biotechnology, South China University of Technology, Guangzhou 510006, China
| | | | - Ruiqi Xu
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Weijian Ye
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Junhua Rao
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xiaosen Guo
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Jihua Sun
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | | | - Chen Ye
- BGI-Shenzhen, Shenzhen 518083, China
| | - Johan van Beusekom
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Espeseth
- Department of Psychology, University of Oslo, 0317 Oslo, Norway.,NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway
| | - Esben Flindt
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Rune M Friborg
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Anders E Halager
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Stephanie Le Hellard
- NORMENT, KG Jebsen Centre for Psychosis Research, Department of Clinical Science, University of Bergen, Bergen 5021, Norway.,Dr E. Martens Research Group of Biological Psychiatry, Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen 5021, Norway
| | - Christina M Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Francesco Lescai
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Shengting Li
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Ole Lund
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Peter Løngren
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Maria Luisa Matey-Hernandez
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ole Mors
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Christian N S Pedersen
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark
| | - Thomas Sicheritz-Pontén
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Patrick Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden.,Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599-7264, USA
| | - Ali Syed
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - David Westergaard
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Rachita Yadav
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Ning Li
- BGI-Europe, Ole Maaløes Vej 3, 2200 Copenhagen, Denmark
| | - Xun Xu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Anders Krogh
- Bioinformatics Centre, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China
| | - Thorkild I A Sørensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark.,Department of Clinical Epidemiology, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, 2000 Frederiksberg, Denmark.,Department of Public Health, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Ramneek Gupta
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Simon Rasmussen
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Søren Besenbacher
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,Department of Clinical Medicine, Aarhus University, 8000 Aarhus, Denmark
| | - Anders D Børglum
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8000 Aarhus, Denmark
| | - Jun Wang
- iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Hans Eiberg
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Karsten Kristiansen
- BGI-Shenzhen, Shenzhen 518083, China.,Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, 2100 Copenhagen, Denmark
| | - Søren Brunak
- DTU Bioinformatics, Department of Bio and Health Informatics, Technical University of Denmark, Kemitorvet, 2800 Kongens Lyngby, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Mikkel Heide Schierup
- Bioinformatics Research Centre, Aarhus University, 8000 Aarhus, Denmark.,iSEQ, Centre for Integrative Sequencing, Aarhus University, 8000 Aarhus, Denmark.,Department of Bioscience, Aarhus University, 8000 Aarhus, Denmark
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17
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Howard DM, Pong-Wong R, Knap PW, Woolliams JA. Use of haplotypes to identify regions harbouring lethal recessive variants in pigs. Genet Sel Evol 2017; 49:57. [PMID: 28709397 PMCID: PMC5512953 DOI: 10.1186/s12711-017-0332-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 07/05/2017] [Indexed: 12/16/2022] Open
Abstract
Background Lethal recessive genetic variants are maintained at relatively low frequencies in a population in the heterozygous state, but by definition are fatal and therefore unobserved in the homozygous state. Since haplotypes allow the tagging of rare and untyped genetic variants, they have potential for studying lethal recessive variants. In this study, we used a large commercial population to identify putative lethal recessive haplotypes that impact either the total number born (TNB) or the number born alive (NBA) as a proportion of the total number born (NBA/TNB). We also compared the use of haplotypes with a single nucleotide polymorphism (SNP)-by-SNP approach and examined the benefits of using additional haplotypes imputed from low-density genotype data for the detection of lethal recessive variants. Candidate haplotypes were identified using population-wide haplotype frequencies and within-family analyses. These candidate haplotypes were subsequently assessed for putative lethal recessive effects on TNB and NBA/TNB by comparing carrier-to-carrier matings with carrier-to-non-carrier matings. Results Using both medium-density and imputed low-density genotype data six regions were identified as containing putative lethal recessive haplotypes that had an effect on TNB. It is likely that these regions were related to at least four putative lethal recessive variants, each located on a different chromosome. Evidence for putative lethal recessive effects on TNB was found on chromosomes 1, 6, 10 and 14 using haplotypes. Using haplotypes from individuals genotyped only at medium-density or a SNP-by-SNP approach did not detect any lethal recessive effects. No lethal recessive haplotypes or SNPs were detected that had an effect on NBA/TNB. Conclusions We show that the use of haplotypes from combining medium-density and imputed low-density genotype data is superior for the identification of lethal recessive variants compared to both a SNP-by-SNP approach and to the use of only medium-density data. We developed a formal statistical framework that provided sufficient power to detect lethal recessive variants in species, which produce large full-sib families, while reducing false positive or type I errors. Applying this framework results in improvements in reproductive performance by purging lethal recessive alleles from a population in a timely and cost-effective manner. Electronic supplementary material The online version of this article (doi:10.1186/s12711-017-0332-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David M Howard
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK.
| | - Ricardo Pong-Wong
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK
| | - Pieter W Knap
- Genus-PIC, Ratsteich 31, 24837, Schleswig, Germany.,Genus PLC, 100 Bluegrass Commons Blvd, Suite 2200, Hendersonville, TN, 37075, USA
| | - John A Woolliams
- The Roslin Institute, R(D)SVS, The University of Edinburgh, Midlothian, UK
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18
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Suk EK, Schulz S, Mentrup B, Huebsch T, Duitama J, Hoehe MR. A Fosmid Pool-Based Next Generation Sequencing Approach to Haplotype-Resolve Whole Genomes. Methods Mol Biol 2017; 1551:223-269. [PMID: 28138850 DOI: 10.1007/978-1-4939-6750-6_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Haplotype resolution of human genomes is essential to describe and interpret genetic variation and its impact on biology and disease. Our approach to haplotyping relies on converting genomic DNA into a fosmid library, which represents the entire diploid genome as a collection of haploid DNA clones of ~40 kb in size. These can be partitioned into pools such that the probability that the same pool contains both parental haplotypes is reduced to ~1 %. This is the key principle of this method, allowing entire pools of fosmids to be massively parallel sequenced, yielding haploid sequence output. Here, we present a detailed protocol for fosmid pool-based next generation sequencing to haplotype-resolve whole genomes including the following steps: (1) generation of high molecular weight DNA fragments of ~40 kb in size from genomic DNA; (2) fosmid cloning and partitioning into 96-well plates; (3) barcoded sequencing library preparation from fosmid pools for next generation sequencing; and (4) computational analysis of fosmid sequences and assembly into contiguous haploid sequences.This method can be used in combination with, but also without, whole genome shotgun sequencing to extensively resolve heterozygous SNPs and structural variants within genomic regions, resulting in haploid contigs of several hundred kb up to several Mb. This method has a broad range of applications including population and ancestry genetics, the clinical interpretation of mutations in personal genomes, the analysis of cancer genomes and highly complex disease gene regions such as MHC. Moreover, haplotype-resolved genome sequencing allows description and interpretation of the diploid nature of genome biology, for example through the analysis of haploid gene forms and allele-specific phenomena. Application of this method has enabled the production of most of the molecular haplotype-resolved genomes reported to date.
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Affiliation(s)
- Eun-Kyung Suk
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Sabrina Schulz
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Birgit Mentrup
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Thomas Huebsch
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
| | - Jorge Duitama
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Margret R Hoehe
- Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195, Berlin, Germany.
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19
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Lehrach H. Omics approaches to individual variation: modeling networks and the virtual patient. DIALOGUES IN CLINICAL NEUROSCIENCE 2016. [PMID: 27757060 PMCID: PMC5067143 DOI: 10.31887/dcns.2016.18.3/hlehrach] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Every human is unique. We differ in our genomes, environment, behavior, disease history, and past and current medical treatment—a complex catalog of differences that often leads to variations in the way each of us responds to a particular therapy. We argue here that true personalization of drug therapies will rely on “virtual patient” models based on a detailed characterization of the individual patient by molecular, imaging, and sensor techniques. The models will be based, wherever possible, on the molecular mechanisms of disease processes and drug action but can also expand to hybrid models including statistics/machine learning/artificial intelligence-based elements trained on available data to address therapeutic areas or therapies for which insufficient information on mechanisms is available. Depending on the disease, its mechanisms, and the therapy, virtual patient models can be implemented at a fairly high level of abstraction, with molecular models representing cells, cell types, or organs relevant to the clinical question, interacting not only with each other but also the environment. In the future, “virtual patient/in-silico self” models may not only become a central element of our health care system, reducing otherwise unavoidable mistakes and unnecessary costs, but also act as “guardian angels” accompanying us through life to protect us against dangers and to help us to deal intelligently with our own health and wellness.
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20
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Analyzing and interpreting genome data at the network level with ConsensusPathDB. Nat Protoc 2016; 11:1889-907. [PMID: 27606777 DOI: 10.1038/nprot.2016.117] [Citation(s) in RCA: 313] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
ConsensusPathDB consists of a comprehensive collection of human (as well as mouse and yeast) molecular interaction data integrated from 32 different public repositories and a web interface featuring a set of computational methods and visualization tools to explore these data. This protocol describes the use of ConsensusPathDB (http://consensuspathdb.org) with respect to the functional and network-based characterization of biomolecules (genes, proteins and metabolites) that are submitted to the system either as a priority list or together with associated experimental data such as RNA-seq. The tool reports interaction network modules, biochemical pathways and functional information that are significantly enriched by the user's input, applying computational methods for statistical over-representation, enrichment and graph analysis. The results of this protocol can be observed within a few minutes, even with genome-wide data. The resulting network associations can be used to interpret high-throughput data mechanistically, to characterize and prioritize biomarkers, to integrate different omics levels, to design follow-up functional assay experiments and to generate topology for kinetic models at different scales.
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Tu J, Lu N, Duan M, Ju A, Sun X, Lu Z. Comparison of the experimental methods in haplotype sequencing via next generation sequencing. QUANTITATIVE BIOLOGY 2016. [DOI: 10.1007/s40484-016-0068-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. Nat Genet 2016; 48:231-237. [PMID: 26808112 PMCID: PMC4942303 DOI: 10.1038/ng.3493] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 12/23/2015] [Indexed: 12/20/2022]
Abstract
An unexpectedly large number of human autosomal genes are subject to monoallelic expression (MAE). Our analysis of 4,227 such genes uncovers surprisingly high genetic variation across human populations. This increased diversity is unlikely to reflect relaxed purifying selection. Remarkably, MAE genes exhibit an elevated recombination rate and an increased density of hypermutable sequence contexts. However, these factors do not fully account for the increased diversity. We find that the elevated nucleotide diversity of MAE genes is also associated with greater allelic age: variants in these genes tend to be older and are enriched in polymorphisms shared by Neanderthals and chimpanzees. Both synonymous and nonsynonymous alleles of MAE genes have elevated average population frequencies. We also observed strong enrichment of the MAE signature among genes reported to evolve under balancing selection. We propose that an important biological function of widespread MAE might be the generation of cell-to-cell heterogeneity; the increased genetic variation contributes to this heterogeneity.
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Abraham PE, Wang X, Ranjan P, Nookaew I, Zhang B, Tuskan GA, Hettich RL. Integrating mRNA and Protein Sequencing Enables the Detection and Quantitative Profiling of Natural Protein Sequence Variants of Populus trichocarpa. J Proteome Res 2015; 14:5318-26. [DOI: 10.1021/acs.jproteome.5b00823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Paul E. Abraham
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Xiaojing Wang
- Department
of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Priya Ranjan
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Intawat Nookaew
- Biological
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Bing Zhang
- Department
of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, United States
| | - Gerald A. Tuskan
- Biological
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Robert L. Hettich
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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Abstract
Human genomes are diploid and, for their complete description and interpretation, it is necessary not only to discover the variation they contain but also to arrange it onto chromosomal haplotypes. Although whole-genome sequencing is becoming increasingly routine, nearly all such individual genomes are mostly unresolved with respect to haplotype, particularly for rare alleles, which remain poorly resolved by inferential methods. Here, we review emerging technologies for experimentally resolving (that is, 'phasing') haplotypes across individual whole-genome sequences. We also discuss computational methods relevant to their implementation, metrics for assessing their accuracy and completeness, and the relevance of haplotype information to applications of genome sequencing in research and clinical medicine.
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