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Kucuk E, van der Sanden BPGH, O'Gorman L, Kwint M, Derks R, Wenger AM, Lambert C, Chakraborty S, Baybayan P, Rowell WJ, Brunner HG, Vissers LELM, Hoischen A, Gilissen C. Comprehensive de novo mutation discovery with HiFi long-read sequencing. Genome Med 2023; 15:34. [PMID: 37158973 PMCID: PMC10169305 DOI: 10.1186/s13073-023-01183-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Long-read sequencing (LRS) techniques have been very successful in identifying structural variants (SVs). However, the high error rate of LRS made the detection of small variants (substitutions and short indels < 20 bp) more challenging. The introduction of PacBio HiFi sequencing makes LRS also suited for detecting small variation. Here we evaluate the ability of HiFi reads to detect de novo mutations (DNMs) of all types, which are technically challenging variant types and a major cause of sporadic, severe, early-onset disease. METHODS We sequenced the genomes of eight parent-child trios using high coverage PacBio HiFi LRS (~ 30-fold coverage) and Illumina short-read sequencing (SRS) (~ 50-fold coverage). De novo substitutions, small indels, short tandem repeats (STRs) and SVs were called in both datasets and compared to each other to assess the accuracy of HiFi LRS. In addition, we determined the parent-of-origin of the small DNMs using phasing. RESULTS We identified a total of 672 and 859 de novo substitutions/indels, 28 and 126 de novo STRs, and 24 and 1 de novo SVs in LRS and SRS respectively. For the small variants, there was a 92 and 85% concordance between the platforms. For the STRs and SVs, the concordance was 3.6 and 0.8%, and 4 and 100% respectively. We successfully validated 27/54 LRS-unique small variants, of which 11 (41%) were confirmed as true de novo events. For the SRS-unique small variants, we validated 42/133 DNMs and 8 (19%) were confirmed as true de novo event. Validation of 18 LRS-unique de novo STR calls confirmed none of the repeat expansions as true DNM. Confirmation of the 23 LRS-unique SVs was possible for 19 candidate SVs of which 10 (52.6%) were true de novo events. Furthermore, we were able to assign 96% of DNMs to their parental allele with LRS data, as opposed to just 20% with SRS data. CONCLUSIONS HiFi LRS can now produce the most comprehensive variant dataset obtainable by a single technology in a single laboratory, allowing accurate calling of substitutions, indels, STRs and SVs. The accuracy even allows sensitive calling of DNMs on all variant levels, and also allows for phasing, which helps to distinguish true positive from false positive DNMs.
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Affiliation(s)
- Erdi Kucuk
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bart P G H van der Sanden
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Luke O'Gorman
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Michael Kwint
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ronny Derks
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | | | | | | | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, The Netherlands
- GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Lisenka E L M Vissers
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
- Department of Internal Medicine, Radboud University Medical Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, the Netherlands.
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, PO Box 9101, 6500 HB, Nijmegen, The Netherlands.
- Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
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Li Q, Zhao L, Zeng Y, Kuang Y, Guan Y, Chen B, Xu S, Tang B, Wu L, Mao X, Sun X, Shi J, Xu P, Diao F, Xue S, Bao S, Meng Q, Yuan P, Wang W, Ma N, Song D, Xu B, Dong J, Mu J, Zhang Z, Fan H, Gu H, Li Q, He L, Jin L, Wang L, Sang Q. Large-scale analysis of de novo mutations identifies risk genes for female infertility characterized by oocyte and early embryo defects. Genome Biol 2023; 24:68. [PMID: 37024973 PMCID: PMC10080761 DOI: 10.1186/s13059-023-02894-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 03/01/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Oocyte maturation arrest and early embryonic arrest are important reproductive phenotypes resulting in female infertility and cause the recurrent failure of assisted reproductive technology (ART). However, the genetic etiologies of these female infertility-related phenotypes are poorly understood. Previous studies have mainly focused on inherited mutations based on large pedigrees or consanguineous patients. However, the role of de novo mutations (DNMs) in these phenotypes remains to be elucidated. RESULTS To decipher the role of DNMs in ART failure and female infertility with oocyte and embryo defects, we explore the landscape of DNMs in 473 infertile parent-child trios and identify a set of 481 confident DNMs distributed in 474 genes. Gene ontology analysis reveals that the identified genes with DNMs are enriched in signaling pathways associated with female reproductive processes such as meiosis, embryonic development, and reproductive structure development. We perform functional assays on the effects of DNMs in a representative gene Tubulin Alpha 4a (TUBA4A), which shows the most significant enrichment of DNMs in the infertile parent-child trios. DNMs in TUBA4A disrupt the normal assembly of the microtubule network in HeLa cells, and microinjection of DNM TUBA4A cRNAs causes abnormalities in mouse oocyte maturation or embryo development, suggesting the pathogenic role of these DNMs in TUBA4A. CONCLUSIONS Our findings suggest novel genetic insights that DNMs contribute to female infertility with oocyte and embryo defects. This study also provides potential genetic markers and facilitates the genetic diagnosis of recurrent ART failure and female infertility.
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Affiliation(s)
- Qun Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
- Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Lin Zhao
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yang Zeng
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Yanping Kuang
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Yichun Guan
- Department of Reproductive Medicine, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Biaobang Chen
- NHC Key Lab of Reproduction Regulation (Shanghai Institute for Biomedical and Pharmaceutical Technologies), Fudan University, Shanghai, 200032, China
| | - Shiru Xu
- Fertility Center, Shenzhen Zhongshan Urology Hospital, Shenzhen, 518001, Guangdong, China
| | - Bin Tang
- Reproductive Medicine Center, The First People's Hospital of Changde City, Changde, 415000, China
| | - Ling Wu
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Xiaoyan Mao
- Reproductive Medicine Center, Shanghai Ninth Hospital, Shanghai Jiao Tong University, Shanghai, 200011, China
| | - Xiaoxi Sun
- Shanghai Ji Ai Genetics and IVF Institute, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, 200011, China
| | - Juanzi Shi
- Reproductive Medicine Center, Northwest Women's and Children's Hospital, Xi'an, 710000, China
| | - Peng Xu
- Hainan Jinghua Hejing Hospital for Reproductive Medicine, Haikou, 570125, China
| | - Feiyang Diao
- Reproductive Medicine Center, Jiangsu Province Hospital, Nanjing, 210036, China
| | - Songguo Xue
- Reproductive Medicine Center, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Shihua Bao
- Department of Reproductive Immunology, Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, 201204, China
| | - Qingxia Meng
- Center for Reproduction and Genetics, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, 215000, China
| | - Ping Yuan
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Wenjun Wang
- IVF Center, Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Ning Ma
- Reproductive Medical Center, Maternal and Child Health Care Hospital of Hainan Province, Haikou, 570206, Hainan Province, China
| | - Di Song
- Naval Medical University, Changhai Hospital, Shanghai, China
| | - Bei Xu
- Reproductive Medicine Centre, Tongji Hospital, Tongji Medical College of Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jie Dong
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Jian Mu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Zhihua Zhang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Huizhen Fan
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Hao Gu
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Qiaoli Li
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China
| | - Lin He
- Bio-X Center, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lei Wang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
| | - Qing Sang
- Institute of Pediatrics, Children's Hospital of Fudan University, the Shanghai Key Laboratory of Medical Epigenetics, the Institutes of Biomedical Sciences, the State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200032, China.
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Ueno S, Hasegawa Y, Kato S, Mori H, Tsukada H, Ohira H, Kaneko S. Rapid survey of de novo mutations in naturally growing tree species following the March 2011 disaster in Fukushima: The effect of low-dose-rate radiation. Environ Int 2023; 174:107893. [PMID: 37058973 DOI: 10.1016/j.envint.2023.107893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/13/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
The impact of low-dose-rate radiation on genetics is largely unknown, particularly in natural environments. The Fukushima Dai-ich Nuclear Power Plant disaster resulted in the creation of contaminated natural lands. In this study, de novo mutations (DNMs) in germ line cells were surveyed from double-digest RADseq fragments in Japanese cedar and flowering cherry trees exposed to ambient dose rates ranging from 0.08 to 6.86 μGy h-1. These two species are among the most widely cultivated Japanese gymnosperm and angiosperm trees for forestry and horticultural purpose, respectively. For Japanese flowering cherry, open crossings were performed to produce seedlings, and only two candidate DNMs were detected from uncontaminated area. For Japanese cedar, the haploid megagametophytes were used as next generation samples. The use of megagametophytes from open crossing for next generation mutation screening had many advantages such as reducing exposure to radiation in contaminated areas because artificial crossings are not needed and the ease of data analysis owing to the haploid nature of megagametophytes. A direct comparison of the nucleotide sequences of parents and megagametophytes revealed an average of 1.4 candidate DNMs per megagametophyte sample (range: 0-40) after filtering procedures were optimized based on the validation of DNMs via Sanger sequencing. There was no relationship between the observed mutations and the ambient dose rate in the growing area or the concentration of 137Cs in cedar branches. The present results also suggest that mutation rates differ among lineages and that the growing environment has a relatively large influence on these mutation rates. These results suggested there was no significant increase in the mutation rate of the germplasm of Japanese cedar and flowering cherry trees growing in the contaminated areas.
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Affiliation(s)
- Saneyoshi Ueno
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan.
| | - Yoichi Hasegawa
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Shuri Kato
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan; Tama Forest Science Garden, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1833-81 Todori, Hachioji, Tokyo 193-0843, Japan
| | - Hideki Mori
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Forest Research and Management Organization, 1 Matsunosato, Tsukuba, Ibaraki 305-8687, Japan
| | - Hirofumi Tsukada
- Institute of Environmental Radioactivity, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan
| | - Hajime Ohira
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan
| | - Shingo Kaneko
- Faculty of Symbiotic Systems Science, Fukushima University, 1 Kanayagawa, Fukushima, Fukushima 960-1296, Japan.
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Sun Y, Wang M, Lin W, Dong W, Xu J. "Mutation blacklist" and "mutation whitelist" of SARS-CoV-2. J Biosaf Biosecur 2022; 4:114-120. [PMID: 35845149 PMCID: PMC9273572 DOI: 10.1016/j.jobb.2022.06.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/21/2022] [Accepted: 06/27/2022] [Indexed: 01/26/2023] Open
Abstract
Over the past two years, scientists throughout the world have completed more than 6 million SARS-CoV-2 genome sequences. Today, the number of SARS-CoV-2 genomes exceeds the total number of all other viral genomes. These genomes are a record of the evolution of SARS-CoV-2 in the human host, and provide information on the emergence of mutations. In this study, analysis of these sequenced genomes identified 296,728 de novo mutations (DNMs), and found that six types of base substitutions reached saturation in the sequenced genome population. Based on this analysis, a "mutation blacklist" of SARS-CoV-2 was compiled. The loci on the "mutation blacklist" are highly conserved, and these mutations likely have detrimental effects on virus survival, replication, and transmission. This information is valuable for SARS-CoV-2 research on gene function, vaccine design, and drug development. Through association analysis of DNMs and viral transmission rates, we identified 185 DNMs that positively correlated with the SARS-CoV-2 transmission rate, and these DNMs where classified as the "mutation whitelist" of SARS-CoV-2. The mutations on the "mutation whitelist" are beneficial for SARS-CoV-2 transmission and could therefore be used to evaluate the transmissibility of new variants. The occurrence of mutations and the evolution of viruses are dynamic processes. To more effectively monitor the mutations and variants of SARS-CoV-2, we built a SARS-CoV-2 mutation and variant monitoring and pre-warning system (MVMPS), which can monitor the occurrence and development of mutations and variants of SARS-CoV-2, as well as provide pre-warning for the prevention and control of SARS-CoV-2 (https://www.omicx.cn/). Additionally, this system could be used in real-time to update the "mutation whitelist" and "mutation blacklist" of SARS-CoV-2.
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Affiliation(s)
- Yamin Sun
- Research Institute of Public Health, Nankai University, Tianjin, PR China
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Min Wang
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, PR China
| | - Wenchao Lin
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Wei Dong
- Research Center for Functional Genomics and Biochip, Tianjin, PR China
| | - Jianguo Xu
- Research Institute of Public Health, Nankai University, Tianjin, PR China
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 202206, PR China
- Research Units of Discovery of Unknown Bacteria and Function, Chinese Academy of Medical Sciences, Beijing 100730, PR China
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Chen WX, Liu B, Zhou L, Xiong X, Fu J, Huang ZF, Tan T, Tang M, Wang J, Tang YP. De novo mutations within metabolism networks of amino acid/protein/energy in Chinese autistic children with intellectual disability. Hum Genomics 2022; 16:52. [PMID: 36320054 PMCID: PMC9623983 DOI: 10.1186/s40246-022-00427-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is often accompanied by intellectual disability (ID). Despite extensive studies, however, the genetic basis for this comorbidity is still not clear. In this study, we tried to develop an analyzing pipeline for de novo mutations and possible pathways related to ID phenotype in ASD. Whole-exome sequencing (WES) was performed to screen de novo mutations and candidate genes in 79 ASD children together with their parents (trios). The de novo altering genes and relative pathways which were associated with ID phenotype were analyzed. The connection nodes (genes) of above pathways were selected, and the diagnostic value of these selected genes for ID phenotype in the study population was also evaluated. RESULTS We identified 89 de novo mutant genes, of which 34 genes were previously reported to be associated with ASD, including double hits in the EGF repeats of NOTCH1 gene (p.V999M and p.S1027L). Interestingly, of these 34 genes, 22 may directly affect intelligence quotient (IQ). Further analyses revealed that these IQ-related genes were enriched in protein synthesis, energy metabolism, and amino acid metabolism, and at least 9 genes (CACNA1A, ALG9, PALM2, MGAT4A, PCK2, PLEKHA1, PSME3, ADI1, and TLE3) were involved in all these three pathways. Seven patients who harbored these gene mutations showed a high prevalence of a low IQ score (< 70), a non-verbal language, and an early diagnostic age (< 4 years). Furthermore, our panel of these 9 genes reached a 10.2% diagnostic rate (5/49) in early diagnostic patients with a low IQ score and also reached a 10% diagnostic yield in those with both a low IQ score and non-verbal language (4/40). CONCLUSION We found some new genetic disposition for ASD accompanied with intellectual disability in this study. Our results may be helpful for etiologic research and early diagnoses of intellectual disability in ASD. Larger population studies and further mechanism studies are warranted.
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Affiliation(s)
- Wen-Xiong Chen
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Bin Liu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.258164.c0000 0004 1790 3548Department of Biobank, Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, Shenzhen, 518102 Guangdong China
| | - Lijie Zhou
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Xiaoli Xiong
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Jie Fu
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Zhi-Fang Huang
- grid.410737.60000 0000 8653 1072The Assessment and Intervention Center for Autistic Children, Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 Guangdong China
| | - Ting Tan
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China
| | - Mingxi Tang
- grid.488387.8Department of Pathology, Affiliated Hospital of Southwest Medical University, Luzhou, 646000 Sichuan China
| | - Jun Wang
- grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China
| | - Ya-Ping Tang
- grid.410737.60000 0000 8653 1072Guangzhou Institute of Pediatrics, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, 510623 China ,grid.412719.8Department of Pediatric Rehabilitation, Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052 China ,grid.12981.330000 0001 2360 039XGuangdong Provincial Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510080 Guangdong China
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陈 曦, 王 斯, 薛 恩, 王 雪, 彭 和, 范 梦, 王 梦, 武 轶, 秦 雪, 李 劲, 吴 涛, 朱 洪, 李 静, 周 治, 陈 大, 胡 永. [Exploring the association between de novo mutations and non-syndromic cleft lip with or without palate based on whole exome sequencing of case-parent trios]. Beijing Da Xue Xue Bao Yi Xue Ban 2022; 54:387-393. [PMID: 35701113 PMCID: PMC9197716 DOI: 10.19723/j.issn.1671-167x.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Indexed: 06/15/2023]
Abstract
OBJECTIVE To explore the association between de novo mutations (DNM) and non-syndromic cleft lip with or without palate (NSCL/P) using case-parent trio design. METHODS Whole-exome sequencing was conducted for twenty-two NSCL/P trios and Genome Analysis ToolKit (GATK) was used to identify DNM by comparing the alleles of the cases and their parents. Information of predictable functions was annotated to the locus with SnpEff. Enrichment analysis for DNM was conducted to test the difference between the actual number and the expected number of DNM, and to explore whether there were genes with more DNM than expected. NSCL/P-related genes indicated by previous studies with solid evidence were selected by literature reviewing. Protein-protein interactions analysis was conducted among the genes with protein-altering DNM and NSCL/P-related genes. R package "denovolyzeR" was used for the enrichment analysis (Bonferroni correction: P=0.05/n, n is the number of genes in the whole genome range). Protein-protein interactions among genes with DNM and genes with solid evidence on the risk factors of NSCL/P were predicted depending on the information provided by STRING database. RESULTS A total of 339 908 SNPs were qualified for the subsequent analysis after quality control. The number of high confident DNM identified by GATK was 345. Among those DNM, forty-four DNM were missense mutations, one DNM was nonsense mutation, two DNM were splicing site mutations, twenty DNM were synonymous mutations and others were located in intron or intergenic regions. The results of enrichment analysis showed that the number of protein-altering DNM on the exome regions was larger than expected (P < 0.05), and five genes (KRTCAP2, HMCN2, ANKRD36C, ADGRL2 and DIPK2A) had more DNM than expected (P < 0.05/(2×19 618)). Protein-protein interaction analysis was conducted among forty-six genes with protein-altering DNM and thirteen genes associated with NSCL/P selected by literature reviewing. Six pairs of interactions occurred between the genes with DNM and known NSCL/P-related genes. The score measuring the confidence level of the predicted interaction between RGPD4 and SUMO1 was 0.868, which was higher than the scores for other pairs of genes. CONCLUSION Our study provided novel insights into the development of NSCL/P and demonstrated that functional analyses of genes carrying DNM were warranted to understand the genetic architecture of complex diseases.
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Affiliation(s)
- 曦 陈
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 斯悦 王
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 恩慈 薛
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 雪珩 王
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 和香 彭
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 梦 范
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 梦莹 王
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 轶群 武
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 雪英 秦
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 劲 李
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 涛 吴
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 洪平 朱
- 北京大学口腔医学院·口腔医院口腔颌面外科,国家口腔医学中心,国家口腔疾病临床医学研究中心,口腔生物材料和数字诊疗装备国家工程研究中心,口腔数字医学北京市重点实验室,国家卫生健康委员会口腔医学计算机应用工程技术研究中心,国家药品监督管理局口腔生物材料重点实验室,北京 100081Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Research Center of Engineering and Technology for Computerized Dentistry & NMPA Key Laboratory for Dental Materials, Beijing 100081, China
| | - 静 李
- 北京大学口腔医学院·口腔医院儿童口腔科,国家口腔医学中心,国家口腔疾病临床医学研究中心,口腔生物材料和数字诊疗装备国家工程研究中心,口腔数字医学北京市重点实验室,国家卫生健康委员会口腔医学计算机应用工程技术研究中心,国家药品监督管理局口腔生物材料重点实验室,北京 100081Department of Pediatric Dentistry, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Research Center of Engineering and Technology for Computerized Dentistry & NMPA Key Laboratory for Dental Materials, Beijing 100081, China
| | - 治波 周
- 北京大学口腔医学院·口腔医院口腔颌面外科,国家口腔医学中心,国家口腔疾病临床医学研究中心,口腔生物材料和数字诊疗装备国家工程研究中心,口腔数字医学北京市重点实验室,国家卫生健康委员会口腔医学计算机应用工程技术研究中心,国家药品监督管理局口腔生物材料重点实验室,北京 100081Department of Oral and Maxillofacial Surgery, Peking University School and Hospital of Stomatology & National Center of Stomatology & National Clinical Research Center for Oral Diseases & National Engineering Research Center of Oral Biomaterials and Digital Medical Devices & Beijing Key Laboratory of Digital Stomatology & NHC Research Center of Engineering and Technology for Computerized Dentistry & NMPA Key Laboratory for Dental Materials, Beijing 100081, China
| | - 大方 陈
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
| | - 永华 胡
- 北京大学公共卫生学院流行病与卫生统计学系,北京 100191Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China
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Sandal P, Jong CJ, Merrill RA, Song J, Strack S. Protein phosphatase 2A - structure, function and role in neurodevelopmental disorders. J Cell Sci 2021; 134:270819. [PMID: 34228795 DOI: 10.1242/jcs.248187] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neurodevelopmental disorders (NDDs), including intellectual disability (ID), autism and schizophrenia, have high socioeconomic impact, yet poorly understood etiologies. A recent surge of large-scale genome or exome sequencing studies has identified a multitude of mostly de novo mutations in subunits of the protein phosphatase 2A (PP2A) holoenzyme that are strongly associated with NDDs. PP2A is responsible for at least 50% of total Ser/Thr dephosphorylation in most cell types and is predominantly found as trimeric holoenzymes composed of catalytic (C), scaffolding (A) and variable regulatory (B) subunits. PP2A can exist in nearly 100 different subunit combinations in mammalian cells, dictating distinct localizations, substrates and regulatory mechanisms. PP2A is well established as a regulator of cell division, growth, and differentiation, and the roles of PP2A in cancer and various neurodegenerative disorders, such as Alzheimer's disease, have been reviewed in detail. This Review summarizes and discusses recent reports on NDDs associated with mutations of PP2A subunits and PP2A-associated proteins. We also discuss the potential impact of these mutations on the structure and function of the PP2A holoenzymes and the etiology of NDDs.
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Affiliation(s)
- Priyanka Sandal
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Chian Ju Jong
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Ronald A Merrill
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Jianing Song
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
| | - Stefan Strack
- Department of Neuroscience and Pharmacology, and Iowa Neuroscience Institute, University of Iowa, Iowa City, Iowa 52242, USA
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Juang JMJ, Lu TP, Su MW, Lin CW, Yang JH, Chu HW, Chen CH, Hsiao YW, Lee CY, Chiang LM, Yu QY, Hsiao CK, Chen CYJ, Wu PE, Pai CH, Chuang EY, Shen CY. Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine. J Adv Res 2021; 30:147-158. [PMID: 34026292 PMCID: PMC8132201 DOI: 10.1016/j.jare.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 12/03/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Introduction A population-specific genomic reference is important for research and clinical practice, yet it remains unavailable for Han Chinese (HC) in Taiwan. Objectives We report the first whole genome sequencing (WGS) database of HC (1000 Taiwanese genome (1KTW-WGS)) and demonstrate several applications to cardiovascular medicine. Methods Whole genomes of 997 HC were sequenced to at least 30X depth. A total of 20,117 relatively healthy HC individuals were genotyped using a customized Axiom GWAS array. We performed a genome-wide genotype imputation technique using IMPUTE2. Results We identified 26.7 million single-nucleotide variants (SNVs) and 4.2 million insertions-deletions. Of the SNVs, 16.1% were novel relative to dbSNP (build 152), and 34.2% were novel relative to gnomAD. A total of 18,450 healthy HC individuals were genotyped using a customized Genome-Wide Association Study (GWAS) array. We identified hypertension-associated variants and developed a hypertension prediction model based on the correlation between the WGS data and GWAS data (combined clinical and genetic models, AUC 0.887), and also identified 3 novel hyperlipidemia-associated variants. Each individual carried an average of 16.42 (SD = 3.72) disease-causing variants. Additionally, we established an online SCN5A (an important cardiac gene) database that can be used to explore racial differences. Finally, pharmacogenetics studies identified HC population-specific SNVs in genes (CYP2C9 and VKORC1) involved in drug metabolism and blood clotting. Conclusion This research demonstrates the benefits of constructing a population-specific genomic reference database for precision medicine.
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Affiliation(s)
- Jyh-Ming Jimmy Juang
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Tzu-Pin Lu
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | | | | | - Jenn-Hwai Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | | | - Chien-Hsiun Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | - Yi-Wen Hsiao
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chien-Yueh Lee
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Mei Chiang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Qi-You Yu
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chuhsing Kate Hsiao
- Department of Public Health, Institute of Epidemiology and Preventative Medicine and Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Ching-Yu Julius Chen
- Cardiovascular Center and Division of Cardiology, Department of Internal Medicine, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei 10002, Taiwan
| | - Pei-Ei Wu
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
| | | | - Eric Y. Chuang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Yang Shen
- Taiwan Biobank, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 11574, Taiwan
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Wang T, Zhang Y, Liu L, Wang Y, Chen H, Fan T, Li J, Xia K, Sun Z. Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes. J Genet Genomics 2021; 48:312-323. [PMID: 33994118 DOI: 10.1016/j.jgg.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 02/06/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a set of complex disorders characterized by diverse and co-occurring clinical symptoms. The genetic contribution in patients with NDDs remains largely unknown. Here, we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations (DNMs) in 86 genes and 2,385 rare inherited mutations (RIMs) with 22 X-linked hemizygotes in 13 genes, 2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes. Furthermore, the DNMs of 16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background. We prioritize 26 novel candidate genes. Notably, six of these genes - ITSN1, UBR3, CADM1, RYR3, FLNA, and PLXNA3 - preferably contribute to autism spectrum disorders (ASDs), as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model. Importantly, these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks. Together, our study expands the genetic spectrum of Chinese NDDs, further facilitating both basic and translational research.
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Affiliation(s)
- Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; DIAGenes Precision Medicine, Beijing 102600, China
| | - Yi Zhang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China
| | - Liqui Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiqian Chen
- Shanghai Adeptus Biotechnology, Shanghai 200126, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China; Department of Neurology, Xiangya Hospital, Central South University, Changsha Hunan, 410083, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, China.
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
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Quaas AM, Kearns WG. Antenatal antioxidants to avert autism? J Assist Reprod Genet 2020; 37:2963-5. [PMID: 33083862 DOI: 10.1007/s10815-020-01982-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 10/23/2022] Open
Abstract
Paternally derived de novo mutations (DNMs) caused by oxidative stress (OS) have been implicated in the development of autism spectrum disorders (ASDs). Whether preconception antioxidant supplementation can reduce the incidence of ASDs by reducing OS is an area of uncertainty and potentially important future scientific investigation.
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Abstract
The genetic architecture of schizophrenia is complex and highly polygenic. This article discusses key findings from genetic studies of childhood-onset schizophrenia (COS) and the more common adult-onset schizophrenia (AOS), including studies of familial aggregation and common, rare, and copy number variants. Extant literature suggests that COS is a rare variant of AOS involving greater familial aggregation of schizophrenia spectrum disorders and a potentially higher occurrence of pathogenic copy number variants. The direct utility of genetics to clinical practice for COS is currently limited; however, identifying common pathways through which risk genes affect brain function offers promise for novel interventions.
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Affiliation(s)
- Jennifer K Forsyth
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA.
| | - Robert F Asarnow
- Department of Psychiatry & Biobehavioral Sciences, University of California, Los Angeles, 760 Westwood Plaza, Los Angeles, CA 90095, USA; Department of Psychology, University of California, Los Angeles, 502 Portola Plaza Los Angeles, CA 90095, USA; Brain Research Institute, University of California, Los Angeles, 695 Charles E Young Dr S, Los Angeles, CA 90095, USA.
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12
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Pan HX, Luo GN, Wan SQ, Qin CL, Tang J, Zhang M, Du M, Xu KK, Shi JQ. Detection of de novo genetic variants in Mayer-Rokitansky-Küster-Hauser syndrome by whole genome sequencing. Eur J Obstet Gynecol Reprod Biol X 2019; 4:100089. [PMID: 31517310 DOI: 10.1016/j.eurox.2019.100089] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 06/09/2019] [Accepted: 07/28/2019] [Indexed: 11/22/2022] Open
Abstract
Objective The aim of this study was to use whole genome sequencing (WGS) help detect de novo mutations or pathogenic genes of Mayer-Rokitansky-Küster-Hauser syndrome type 1(MRKH syndrome type 1). Study design This was a case-parent trios study. Nine unrelated probands, with MRKH syndrome type 1 and their parents were enrolled. The enrollment, sequencing process, establishment of the de novo mutations detecting procedure and experiment part were performed over a 2-year period. Results we detected 632 de novo single nucleotide variants (SNVs), 267 de novo small insertions/deletions (indels), 39 de novo structural variations (SVs) and 28 de novo copy number alterations (CNAs). Three novel damaging coding de novo SNVs with three damaging coding de novo genes (PIK3CD, SLC4A10 and TNK2) were revealed. Two SNVs were annotated of the promoter region of gene NBPF10 and 3'UTR of NOTCH2NL, potentially contributing to the pathogenesis of MRKH. Conclusion We identified five de novo mutations in BAZ2B, KLHL18, PIK3CD, SLC4A10 and TNK2 by performing WGS, the functional involvement of all deleterious mutations in MRKH candidate genes of the trios warrant further study. WGS may complement conventional array to capture the complete landscape of the genome in MRKH.
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Denisova K. Failure to attune to language predicts autism in high risk infants. Brain Lang 2019; 194:109-120. [PMID: 31133435 DOI: 10.1016/j.bandl.2019.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 06/09/2023]
Abstract
Young humans are typically sensitive to evolutionarily important aspects of information in the surrounding environment in a way that makes us thrive. Seeking to probe the putative disruptions of this process in infancy, I examined the statistical character of head movements in 52 9-10 mo-old infants, half at high familial risk (HR) for Autism Spectrum Disorders (ASD), who underwent an fMRI scan while listening to words spoken with alternating stress patterns on syllables. Relative to low risk (LR) infants, HR infants, in particular those showing the least rapid receptive language progress, had significantly lower noise-to-signal levels and increased symmetry. A comparison of patterns during a native language and a sleep scan revealed the most atypical ordering of signatures on the 3 tasks in a subset of HR infants, suggesting that the biological mechanism of language development is least acquisitive in those HR infants who go on to develop ASD in toddlerhood.
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Affiliation(s)
- Kristina Denisova
- Sackler Institute for Developmental Psychobiology, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Department of Psychiatry, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA; Division of Developmental Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA.
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Hernandez CC, Macdonald RL. A structural look at GABA A receptor mutations linked to epilepsy syndromes. Brain Res 2019; 1714:234-247. [PMID: 30851244 DOI: 10.1016/j.brainres.2019.03.004] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Revised: 02/25/2019] [Accepted: 03/06/2019] [Indexed: 12/12/2022]
Abstract
Understanding the genetic variation in GABAA receptor subunit genes (GABRs), GABRA1-6, GABRB1-3, GABRG1-3 and GABRD, in individuals affected by epilepsy may improve the diagnosis and treatment of epilepsy syndromes through identification of disease-associated variants. However, the lack of functional analysis and validation of many novel and previously reported familial and de novo mutations have made it challenging to address meaningful gene associations with epilepsy syndromes. GABAA receptors belong to the Cys-loop receptor family. Even though GABAA receptor mutant residues are widespread among different GABRs, their frequent occurrence in important structural domains that share common functional features suggests associations between structure and function.
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Affiliation(s)
- Ciria C Hernandez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
| | - Robert L Macdonald
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
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15
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Guo H, Wang T, Wu H, Long M, Coe BP, Li H, Xun G, Ou J, Chen B, Duan G, Bai T, Zhao N, Shen Y, Li Y, Wang Y, Zhang Y, Baker C, Liu Y, Pang N, Huang L, Han L, Jia X, Liu C, Ni H, Yang X, Xia L, Chen J, Shen L, Li Y, Zhao R, Zhao W, Peng J, Pan Q, Long Z, Su W, Tan J, Du X, Ke X, Yao M, Hu Z, Zou X, Zhao J, Bernier RA, Eichler EE, Xia K. Inherited and multiple de novo mutations in autism/developmental delay risk genes suggest a multifactorial model. Mol Autism 2018; 9:64. [PMID: 30564305 PMCID: PMC6293633 DOI: 10.1186/s13229-018-0247-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 11/23/2018] [Indexed: 11/17/2022] Open
Abstract
Background We previously performed targeted sequencing of autism risk genes in probands from the Autism Clinical and Genetic Resources in China (ACGC) (phase I). Here, we expand this analysis to a larger cohort of patients (ACGC phase II) to better understand the prevalence, inheritance, and genotype-phenotype correlations of likely gene-disrupting (LGD) mutations for autism candidate genes originally identified in cohorts of European descent. Methods We sequenced 187 autism candidate genes in an additional 784 probands and 85 genes in 599 probands using single-molecule molecular inversion probes. We tested the inheritance of potentially pathogenic mutations, performed a meta-analysis of phase I and phase II data and combined our results with existing exome sequence data to investigate the phenotypes of carrier parents and patients with multiple hits in different autism risk genes. Results We validated recurrent, LGD, de novo mutations (DNMs) in 13 genes. We identified a potential novel risk gene (ZNF292), one novel gene with recurrent LGD DNMs (RALGAPB), as well as genes associated with macrocephaly (GIGYF2 and WDFY3). We identified the transmission of private LGD mutations in genes predominantly associated with DNMs and showed that parental carriers tended to share milder autism-related phenotypes. Patients that carried DNMs in two or more candidate genes show more severe phenotypes. Conclusions We identify new risk genes and transmission of deleterious mutations in genes primarily associated with DNMs. The fact that parental carriers show milder phenotypes and patients with multiple hits are more severe supports a multifactorial model of risk.
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Affiliation(s)
- Hui Guo
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Tianyun Wang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Huidan Wu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Min Long
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Honghui Li
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi China
| | - Guanglei Xun
- Mental Health Center of Shandong Province, Jinan, Shandong China
| | - Jianjun Ou
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Biyuan Chen
- Children Development Behavior Center of the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Guiqin Duan
- Center of Children Psychology and Behavior, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Ting Bai
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Ningxia Zhao
- Xi’an Encephalopathy Hospital of Traditional Chinese Medicine, Xi’an, Shaanxi China
| | - Yidong Shen
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan China
| | - Yun Li
- Child Mental Health Research Center, Nanjing Brain Hospital Affiliated of Nanjing Medical University, Nanjing, Jiangsu China
| | - Yazhe Wang
- Center of Children Psychology and Behavior, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Yu Zhang
- Key Laboratory of Developmental Disorders in Children, Liuzhou Maternity and Child Healthcare Hospital, Liuzhou, Guangxi China
| | - Carl Baker
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
| | - Yanling Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Nan Pang
- Department of Pediatrics, the Xiangya Hospital, Central South University, Changsha, China
| | - Lian Huang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Lin Han
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Xiangbin Jia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Cenying Liu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Hailun Ni
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Xinyi Yang
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Lu Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Jingjing Chen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Lu Shen
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Ying Li
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Rongjuan Zhao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Wenjing Zhao
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Jing Peng
- Department of Pediatrics, the Xiangya Hospital, Central South University, Changsha, China
| | - Qian Pan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Zhigao Long
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Wei Su
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Jieqiong Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Xiaogang Du
- Xi’an Encephalopathy Hospital of Traditional Chinese Medicine, Xi’an, Shaanxi China
| | - Xiaoyan Ke
- Child Mental Health Research Center, Nanjing Brain Hospital Affiliated of Nanjing Medical University, Nanjing, Jiangsu China
| | - Meiling Yao
- Center of Children Psychology and Behavior, the Third Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan China
| | - Zhengmao Hu
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
| | - Xiaobing Zou
- Children Development Behavior Center of the Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong China
| | - Jingping Zhao
- Mental Health Institute of the Second Xiangya Hospital, Central South University, Changsha, Hunan China
| | | | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA USA
| | - Kun Xia
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan China
- Key Laboratory of Medical Information Research, Central South University, Changsha, Hunan China
- Collaborative Innovation Center for Genetics and Development, Shanghai, China
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16
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Wu J, Yu P, Jin X, Xu X, Li J, Li Z, Wang M, Wang T, Wu X, Jiang Y, Cai W, Mei J, Min Q, Xu Q, Zhou B, Guo H, Wang P, Zhou W, Hu Z, Li Y, Cai T, Wang Y, Xia K, Jiang YH, Sun ZS. Genomic landscapes of Chinese sporadic autism spectrum disorders revealed by whole-genome sequencing. J Genet Genomics 2018; 45:527-538. [PMID: 30392784 DOI: 10.1016/j.jgg.2018.09.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 08/25/2018] [Accepted: 09/09/2018] [Indexed: 12/12/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with considerable clinical and genetic heterogeneity. In this study, we identified all classes of genomic variants from whole-genome sequencing (WGS) dataset of 32 Chinese trios with ASD, including de novo mutations, inherited variants, copy number variants (CNVs) and genomic structural variants. A higher mutation rate (Poisson test, P < 2.2 × 10-16) in exonic (1.37 × 10-8) and 3'-UTR regions (1.42 × 10-8) was revealed in comparison with that of whole genome (1.05 × 10-8). Using an integrated model, we identified 87 potentially risk genes (P < 0.01) from 4832 genes harboring various rare deleterious variants, including CHD8 and NRXN2, implying that the disorders may be in favor to multiple-hit. In particular, frequent rare inherited mutations of several microcephaly-associated genes (ASPM, WDR62, and ZNF335) were found in ASD. In chromosomal structure analyses, we found four de novo CNVs and one de novo chromosomal rearrangement event, including a de novo duplication of UBE3A-containing region at 15q11.2-q13.1, which causes Angelman syndrome and microcephaly, and a disrupted TNR due to de novo chromosomal translocation t(1; 5)(q25.1; q33.2). Taken together, our results suggest that abnormalities of centrosomal function and chromatin remodeling of the microcephaly-associated genes may be implicated in pathogenesis of ASD. Adoption of WGS as a new yet efficient technique to illustrate the full genetic spectrum in complex disorders, such as ASD, could provide novel insights into pathogenesis, diagnosis and treatment.
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Affiliation(s)
- Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Ping Yu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Jin
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xiu Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Jinchen Li
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | | | - Tao Wang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Xueli Wu
- BGI-Shenzhen, Shenzhen 518083, China
| | - Yi Jiang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Wanshi Cai
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Junpu Mei
- BGI-Shenzhen, Shenzhen 518083, China
| | - Qingjie Min
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Qiong Xu
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Bingrui Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Hui Guo
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | - Ping Wang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Wenhao Zhou
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Zhengmao Hu
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China
| | | | - Tao Cai
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Yi Wang
- Department of Child Healthcare, Children's Hospital of Fudan University, Shanghai 200032, China
| | - Kun Xia
- State Key Laboratory of Medical Genetics, Central South University, Changsha 410078, China.
| | - Yong-Hui Jiang
- Department of Pediatrics and Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Zhong Sheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China.
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17
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Buena-Atienza E, Nasser F, Kohl S, Wissinger B. A 73,128 bp de novo deletion encompassing the OPN1LW/OPN1MW gene cluster in sporadic Blue Cone Monochromacy: a case report. BMC Med Genet 2018; 19:107. [PMID: 29940872 PMCID: PMC6019650 DOI: 10.1186/s12881-018-0623-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 06/12/2018] [Indexed: 01/04/2023]
Abstract
Background Blue Cone Monochromacy (BCM) is a rare congenital cone dysfunction disorder with X-linked recessive mode of inheritance. BCM is caused by mutations at the OPN1LW/MW cone opsin gene cluster including deletions of the locus control region (LCR) and/or parts of the gene cluster. We aimed at investigating the clinical presentation, genetic cause and inheritance underlying a sporadic case of BCM. Case presentation We report a 24-year-old male presenting with congenital photophobia, nystagmus and colour vision abnormalities. There was no history of retinal dystrophy in the family. Clinical diagnosis of BCM was supported by genetic investigations of the patient and his family members. Molecular genetic analysis of the OPN1LW/OPN1MW gene cluster revealed a novel deletion of about 73 kb in the patient encompassing the LCR. The deletion was absent in the X-chromosomes of both the mother and transmitting grandfather. Conclusions The present report provides the clinical findings and the genetic basis underlying a sporadic BCM case which is caused by a de novo deletion within the OPN1LW/MW gene cluster originating from the mother’s germline due to Alu-repeat mediated recombination. This is the first report of a de novo deletion resulting in BCM, highlighting the importance to consider BCM and perform genetic testing for this condition in male patients with cone dysfunction also in the absence of a positive family history.
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Affiliation(s)
- Elena Buena-Atienza
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Elfriede-Aulhorn 7, D-72076, Tuebingen, Germany
| | - Fadi Nasser
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Elfriede-Aulhorn 7, D-72076, Tuebingen, Germany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Elfriede-Aulhorn 7, D-72076, Tuebingen, Germany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tuebingen, Elfriede-Aulhorn 7, D-72076, Tuebingen, Germany.
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18
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Webster RJ, Williams A, Marchetti F, Yauk CL. Discovering human germ cell mutagens with whole genome sequencing: Insights from power calculations reveal the importance of controlling for between-family variability. Mutat Res Genet Toxicol Environ Mutagen 2018; 831:24-32. [PMID: 29875074 DOI: 10.1016/j.mrgentox.2018.04.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/09/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022]
Abstract
Mutations in germ cells pose potential genetic risks to offspring. However, de novo mutations are rare events that are spread across the genome and are difficult to detect. Thus, studies in this area have generally been under-powered, and no human germ cell mutagen has been identified. Whole Genome Sequencing (WGS) of human pedigrees has been proposed as an approach to overcome these technical and statistical challenges. WGS enables analysis of a much wider breadth of the genome than traditional approaches. Here, we performed power analyses to determine the feasibility of using WGS in human families to identify germ cell mutagens. Different statistical models were compared in the power analyses (ANOVA and multiple regression for one-child families, and mixed effect model sampling between two to four siblings per family). Assumptions were made based on parameters from the existing literature, such as the mutation-by-paternal age effect. We explored two scenarios: a constant effect due to an exposure that occurred in the past, and an accumulating effect where the exposure is continuing. Our analysis revealed the importance of modeling inter-family variability of the mutation-by-paternal age effect. Statistical power was improved by models accounting for the family-to-family variability. Our power analyses suggest that sufficient statistical power can be attained with 4-28 four-sibling families per treatment group, when the increase in mutations ranges from 40 to 10% respectively. Modeling family variability using mixed effect models provided a reduction in sample size compared to a multiple regression approach. Much larger sample sizes were required to detect an interaction effect between environmental exposures and paternal age. These findings inform study design and statistical modeling approaches to improve power and reduce sequencing costs for future studies in this area.
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Affiliation(s)
- R J Webster
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - A Williams
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - F Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada
| | - C L Yauk
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON, K1A 0K9, Canada.
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19
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Abstract
PURPOSE To examine current evidence of the known effects of advanced paternal age on sperm genetic and epigenetic changes and associated birth defects and diseases in offspring. METHODS Review of published PubMed literature. RESULTS Advanced paternal age (> 40 years) is associated with accumulated damage to sperm DNA and mitotic and meiotic quality control mechanisms (mismatch repair) during spermatogenesis. This in turn causes well-delineated abnormalities in sperm chromosomes, both numerical and structural, and increased sperm DNA fragmentation (3%/year of age) and single gene mutations (relative risk, RR 10). An increase in related abnormalities in offspring has also been described, including miscarriage (RR 2) and fetal loss (RR 2). There is also a significant increase in rare, single gene disorders (RR 1.3 to 12) and congenital anomalies (RR 1.2) in offspring. Current research also suggests that autism, schizophrenia, and other forms of "psychiatric morbidity" are more likely in offspring (RR 1.5 to 5.7) with advanced paternal age. Genetic defects related to faulty sperm quality control leading to single gene mutations and epigenetic alterations in several genetic pathways have been implicated as root causes. CONCLUSIONS Advanced paternal age is associated with increased genetic and epigenetic risk to offspring. However, the precise age at which risk develops and the magnitude of the risk are poorly understood or may have gradual effects. Currently, there are no clinical screenings or diagnostic panels that target disorders associated with advanced paternal age. Concerned couples and care providers should pursue or recommend genetic counseling and prenatal testing regarding specific disorders.
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Affiliation(s)
- Alexander N. Yatsenko
- Department of OB/GYN and Reproductive Sciences, School of Medicine, University of Pittsburgh, 204 Craft Avenue, Room A206, Pittsburgh, PA 15213 USA
| | - Paul J. Turek
- The Turek Clinics, 55 Francisco St., Suite 300, San Francisco, CA 94133 USA
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20
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Lin GN, Corominas R, Nam HJ, Urresti J, Iakoucheva LM. Comprehensive Analyses of Tissue-Specific Networks with Implications to Psychiatric Diseases. Methods Mol Biol 2018; 1613:371-402. [PMID: 28849569 DOI: 10.1007/978-1-4939-7027-8_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent advances in genome sequencing and "omics" technologies are opening new opportunities for improving diagnosis and treatment of human diseases. The precision medicine initiative in particular aims at developing individualized treatment options that take into account individual variability in genes and environment of each person. Systems biology approaches that group genes, transcripts and proteins into functionally meaningful networks will play crucial role in the future of personalized medicine. They will allow comparison of healthy and disease-affected tissues and organs from the same individual, as well as between healthy and disease-afflicted individuals. However, the field faces a multitude of challenges ranging from data integration to statistical and combinatorial issues in data analyses. This chapter describes computational approaches developed by us and the others to tackle challenges in tissue-specific network analyses, with the main focus on psychiatric diseases.
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Affiliation(s)
- Guan Ning Lin
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive #0603, La Jolla, CA, 92093, USA.,Shanghai Mental Health Center, Shanghai Key Laboratory of Psychotic Disorders and School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Roser Corominas
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive #0603, La Jolla, CA, 92093, USA.,Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Hyun-Jun Nam
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive #0603, La Jolla, CA, 92093, USA
| | - Jorge Urresti
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive #0603, La Jolla, CA, 92093, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, 9500 Gilman Drive #0603, La Jolla, CA, 92093, USA.
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21
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Li SJ, Yu SS, Luo HY, Li X, Rao B, Wang Y, Li ZZ, Liu G, Zou LP, Zhang JS, Feng C, Liu J, Liu JW, Hu N, Chen XQ, Yu SY, Li K, He MW, Yu XG, Wang J, Guo SL, Chen ZY, Zhang L, Ma L. Two de novo variations identified by massively parallel sequencing in 13 Chinese families with children diagnosed with autism spectrum disorder. Clin Chim Acta 2018; 479:144-147. [PMID: 29366832 DOI: 10.1016/j.cca.2018.01.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 01/10/2018] [Accepted: 01/16/2018] [Indexed: 01/09/2023]
Abstract
Autism spectrum disorder (ASD) is a genetically heterogeneous neurodevelopmental disorder characterized by impairments in social interaction and communication, and by restricted and repetitive behaviors. The genetic architecture of ASD has been elucidated, including chromosomal rearrangements, de novo or inherited rare variants, and copy number variants. However, the genetic mechanism of Chinese families with ASD children is explored rarely. To identify genetic pathogenesis, we performed massively parallel sequencing on 13 Chinese ASD trio families, and found two de novo variations. The novel de novo splice alteration c.664 + 2T > G in the DEAF1 gene and the novel de novo missense mutation c.95 C > T in the AADAT gene associated with ASD may be important clues for exploring the etiology of this disorder.
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Affiliation(s)
- Shi-Jun Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China.
| | | | | | - Xin Li
- BGI-shenzhen, Shenzhen 518083, China
| | - Bin Rao
- BGI-shenzhen, Shenzhen 518083, China
| | - Yi Wang
- Department of Stomatology, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhen-Zhen Li
- Department of Medical Instruments, Chinese PLA General Hospital, Beijing 100853, China
| | - Gang Liu
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Li-Ping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Ji-Shui Zhang
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Chen Feng
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Jing Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Jian-Wei Liu
- Institute of Geriatric Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Nan Hu
- Department of Rehabilitation Medicine, Chinese PLA General Hospital, Beijing 100853, China
| | - Xiao-Qiao Chen
- Department of Neurology, Beijing Children's Hospital of Capital Medical University, Beijing 100045, China
| | - Sheng-Yuan Yu
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Ke Li
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Mian-Wang He
- Department of Neurology, Chinese PLA General Hospital, Beijing 100853, China
| | - Xin-Guang Yu
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Jun Wang
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Sheng-Li Guo
- Department of Neurosurgery, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi-Ye Chen
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
| | - Lei Zhang
- Department of Medical Information, Chinese PLA General Hospital, Beijing 100853, China
| | - Lin Ma
- Department of Radiology, Chinese PLA General Hospital, Beijing 100853, China
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22
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Nguyen HT, Bryois J, Kim A, Dobbyn A, Huckins LM, Munoz-Manchado AB, Ruderfer DM, Genovese G, Fromer M, Xu X, Pinto D, Linnarsson S, Verhage M, Smit AB, Hjerling-Leffler J, Buxbaum JD, Hultman C, Sklar P, Purcell SM, Lage K, He X, Sullivan PF, Stahl EA. Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders. Genome Med 2017; 9:114. [PMID: 29262854 PMCID: PMC5738153 DOI: 10.1186/s13073-017-0497-y] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Accepted: 11/16/2017] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Integrating rare variation from trio family and case-control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified. METHODS We used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls). RESULTS For SCZ, we estimate there are 1,551 risk genes. There are more risk genes and they have weaker effects than for NDDs. We provide power analyses to predict the number of risk-gene discoveries as more data become available. We confirm and augment prior risk gene and gene set enrichment results for SCZ and NDDs. In particular, we detected 98 new DD risk genes at FDR < 0.05. Correlations of risk-gene posterior probabilities are high across four NDDs (ρ>0.55), but low between SCZ and the NDDs (ρ<0.3). An in-depth analysis of 288 NDD genes shows there is highly significant protein-protein interaction (PPI) network connectivity, and functionally distinct PPI subnetworks based on pathway enrichment, single-cell RNA-seq cell types, and multi-region developmental brain RNA-seq. CONCLUSIONS We have extended a pipeline used in ASD studies and applied it to infer rare genetic parameters for SCZ and four NDDs ( https://github.com/hoangtn/extTADA ). We find many new DD risk genes, supported by gene set enrichment and PPI network connectivity analyses. We find greater similarity among NDDs than between NDDs and SCZ. NDD gene subnetworks are implicated in postnatally expressed presynaptic and postsynaptic genes, and for transcriptional and post-transcriptional gene regulation in prenatal neural progenitor and stem cells.
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Affiliation(s)
- Hoang T. Nguyen
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Julien Bryois
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - April Kim
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Amanda Dobbyn
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Laura M. Huckins
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Ana B. Munoz-Manchado
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Douglas M. Ruderfer
- Division of Genetic Medicine, Departments of Medicine, Psychiatry and Biomedical Informatics, Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, 37235 TN USA
| | - Giulio Genovese
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Genetics, Harvard Medical School, Cambridge, Massachusetts USA
| | - Menachem Fromer
- Verily Life Sciences, 269 E Grand Ave, South San Francisco, 94080 CA USA
| | - Xinyi Xu
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Dalila Pinto
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Sten Linnarsson
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Matthijs Verhage
- Department of Functional Genomics, The Center for Neurogenomics and Cognitive Research, VU University and VU Medical Center, Amsterdam, The Netherlands
| | - August B. Smit
- Department of Molecular and Cellular Neurobiology, The Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
| | - Jens Hjerling-Leffler
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, SE-17177 Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Christina Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Pamela Sklar
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
| | - Shaun M. Purcell
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Sleep Center, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts USA
| | - Kasper Lage
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
- Department of Surgery, Massachusetts General Hospital, Boston, 02114 MA USA
| | - Xin He
- Department of Human Genetics, University of Chicago, Chicago, 60637 IL USA
| | - Patrick F. Sullivan
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Departments of Genetics and Psychiatry, University of North Carolina, Chapel Hill, 27599-7264 North Carolina USA
| | - Eli A. Stahl
- Division of Psychiatric Genomics, Department of Genetics and Genomic Sciences, Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, 10029 NY USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts USA
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23
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Abstract
Next-generation sequencing (NGS) is now more accessible to clinicians and researchers. As a result, our understanding of the genetics of neurodevelopmental disorders (NDDs) has rapidly advanced over the past few years. NGS has led to the discovery of new NDD genes with an excess of recurrent de novo mutations (DNMs) when compared to controls. Development of large-scale databases of normal and disease variation has given rise to metrics exploring the relative tolerance of individual genes to human mutation. Genetic etiology and diagnosis rates have improved, which have led to the discovery of new pathways and tissue types relevant to NDDs. In this review, we highlight several key findings based on the discovery of recurrent DNMs ranging from copy number variants to point mutations. We explore biases and patterns of DNM enrichment and the role of mosaicism and secondary mutations in variable expressivity. We discuss the benefit of whole-genome sequencing (WGS) over whole-exome sequencing (WES) to understand more complex, multifactorial cases of NDD and explain how this improved understanding aids diagnosis and management of these disorders. Comprehensive assessment of the DNM landscape across the genome using WGS and other technologies will lead to the development of novel functional and bioinformatics approaches to interpret DNMs and drive new insights into NDD biology.
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Affiliation(s)
- Amy B Wilfert
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, 98195, USA.
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98195, USA.
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24
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Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RWW, Burns AJ, Cherny SS, Dopazo J, Eggen BJL, Griseri P, Jalloh B, Le TL, Lui VCH, Luzón-Toro B, Matera I, Ngan ESW, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CSM, van den Hout MCGN, van der Linde HC, van Ham TJ, van IJcken WFJ, Verheij JBGM, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PKH, Garcia-Barceló MM, Hofstra RMW. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biol 2017; 18:48. [PMID: 28274275 PMCID: PMC5343413 DOI: 10.1186/s13059-017-1174-6] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 12/17/2022] Open
Abstract
Background Hirschsprung disease (HSCR), which is congenital obstruction of the bowel, results from a failure of enteric nervous system (ENS) progenitors to migrate, proliferate, differentiate, or survive within the distal intestine. Previous studies that have searched for genes underlying HSCR have focused on ENS-related pathways and genes not fitting the current knowledge have thus often been ignored. We identify and validate novel HSCR genes using whole exome sequencing (WES), burden tests, in silico prediction, unbiased in vivo analyses of the mutated genes in zebrafish, and expression analyses in zebrafish, mouse, and human. Results We performed de novo mutation (DNM) screening on 24 HSCR trios. We identify 28 DNMs in 21 different genes. Eight of the DNMs we identified occur in RET, the main HSCR gene, and the remaining 20 DNMs reside in genes not reported in the ENS. Knockdown of all 12 genes with missense or loss-of-function DNMs showed that the orthologs of four genes (DENND3, NCLN, NUP98, and TBATA) are indispensable for ENS development in zebrafish, and these results were confirmed by CRISPR knockout. These genes are also expressed in human and mouse gut and/or ENS progenitors. Importantly, the encoded proteins are linked to neuronal processes shared by the central nervous system and the ENS. Conclusions Our data open new fields of investigation into HSCR pathology and provide novel insights into the development of the ENS. Moreover, the study demonstrates that functional analyses of genes carrying DNMs are warranted to delineate the full genetic architecture of rare complex diseases. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1174-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongsheng Gui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Duco Schriemer
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - William W Cheng
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.,Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rajendra K Chauhan
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Guillermo Antiňolo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Courtney Berrios
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Marta Bleda
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain.,Department of Medicine, School of Clinical Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, UK
| | - Alice S Brooks
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Erasmus Center for Biomics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Alan J Burns
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK
| | - Stacey S Cherny
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Joaquin Dopazo
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Bart J L Eggen
- Department of Neuroscience, section Medical Physiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | | | - Binta Jalloh
- Department of Biology, Emory University, Atlanta, USA
| | - Thuy-Linh Le
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Vincent C H Lui
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Berta Luzón-Toro
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Ivana Matera
- UOC Genetica Medica, Istituto Gaslini, Genoa, Italy
| | - Elly S W Ngan
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Anna Pelet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Macarena Ruiz-Ferrer
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | - Pak C Sham
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Man-Ting So
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Yunia Sribudiani
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands.,Department of Biochemistry and Molecular Biology, Faculty of Medicine, Universitas Padjadjaran, Bandung, Indonesia
| | - Clara S M Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | | | - Herma C van der Linde
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | - Tjakko J van Ham
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands
| | | | - Joke B G M Verheij
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Salud Borrego
- Department of Genetics, Reproduction and Fetal Medicine, Institute of Biomedicine of Seville (IBIS), University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.,Centre for Biomedical Network Research on Rare Diseases (CIBERER), Seville, Spain
| | | | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Stanislas Lyonnet
- Laboratory of embryology and genetics of human malformations, INSERM UMR 1163, Institut Imagine, Paris, France.,Department of Genetics, Paris Descartes-Sorbonne Paris Cité University, Hôpital Necker-Enfants Malades (APHP), Paris, France
| | - Paul K H Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China
| | - Maria-Mercè Garcia-Barceló
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR, China.
| | - Robert M W Hofstra
- Department of Clinical Genetics, Erasmus University Medical Center, PO Box 2040, 3000CA, Rotterdam, The Netherlands. .,Stem Cells and Regenerative Medicine, Birth Defects Research Centre, UCL Institute of Child Health, London, UK.
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25
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Boitrelle F, Plouvier P, Dumont A, Barbotin AL, Rigot JM, Belaïsch-Allart J, Robin G. [Effects of father's age on fertility, results of ART and health of children]. ACTA ACUST UNITED AC 2017; 45:28-31. [PMID: 28238311 DOI: 10.1016/j.gofs.2016.12.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 09/09/2016] [Indexed: 10/20/2022]
Abstract
Many studies exist on the impact of female age on fertility, success of assisted reproductive technologies and on obstetric, fetal and neonatal adverse outcomes. Late paternity seems commonplace especially in the media… But there are reliable scientific data which confirm decline of fertility related to male age but also an increased risk of genetic diseases for the offspring. The objective of this article is to make a synthesis of the literature on this subject.
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Affiliation(s)
- F Boitrelle
- Laboratoire de biologie de la reproduction, CHI de Poissy-Saint-Germain-en-Laye, 78303 Poissy, France; EA 7404 GIG, faculté des sciences de la santé Simone-Veil, 78180 Montigny-Le-Bretonneux, France
| | - P Plouvier
- Service de gynécologie endocrinienne et médecine de la reproduction, hôpital Jeanne-de-Flandre, CHRU de Lille, avenue Eugène-Avinée, 59037 Lille cedex, France
| | - A Dumont
- Service de gynécologie endocrinienne et médecine de la reproduction, hôpital Jeanne-de-Flandre, CHRU de Lille, avenue Eugène-Avinée, 59037 Lille cedex, France
| | - A-L Barbotin
- Service de biologie de la reproduction-histologie-embryologie, hôpital Jeanne-de-Flandre, CHRU de Lille, avenue Eugène-Avinée, 59037 Lille cedex, France; EA 4308 gamétogenèse et qualité du gamète, institut de biologie de la reproduction-spermiologie-CECOS, hôpital Albert-Calmette, centre hospitalier régional universitaire, 59000 Lille, France
| | - J-M Rigot
- EA 4308 gamétogenèse et qualité du gamète, institut de biologie de la reproduction-spermiologie-CECOS, hôpital Albert-Calmette, centre hospitalier régional universitaire, 59000 Lille, France; Service d'andrologie, hôpital Albert-Calmette, CHRU de Lille, boulevard Jules-Leclercq, 59037 Lille cedex, France
| | - J Belaïsch-Allart
- Service de gynécologie-obstétrique et assistance médicale à la procréation, centre hospitalier des Quatre-Villes, rue Lauer, 92210 Saint-Cloud, France
| | - G Robin
- Service de gynécologie endocrinienne et médecine de la reproduction, hôpital Jeanne-de-Flandre, CHRU de Lille, avenue Eugène-Avinée, 59037 Lille cedex, France; EA 4308 gamétogenèse et qualité du gamète, institut de biologie de la reproduction-spermiologie-CECOS, hôpital Albert-Calmette, centre hospitalier régional universitaire, 59000 Lille, France; Service d'andrologie, hôpital Albert-Calmette, CHRU de Lille, boulevard Jules-Leclercq, 59037 Lille cedex, France.
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26
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Stevens SJC, van Essen AJ, van Ravenswaaij CMA, Elias AF, Haven JA, Lelieveld SH, Pfundt R, Nillesen WM, Yntema HG, van Roozendaal K, Stegmann AP, Gilissen C, Brunner HG. Truncating de novo mutations in the Krüppel-type zinc-finger gene ZNF148 in patients with corpus callosum defects, developmental delay, short stature, and dysmorphisms. Genome Med 2016; 8:131. [PMID: 27964749 PMCID: PMC5155377 DOI: 10.1186/s13073-016-0386-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 12/01/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Krüppel-type zinc finger genes (ZNF) constitute a large yet relatively poorly characterized gene family. ZNF genes encode proteins that recognize specific DNA motifs in gene promotors. They act as transcriptional co-activators or -repressors via interaction with chromatin remodeling proteins and other transcription factors. Only few ZNF genes are currently linked to human disorders and identification of ZNF gene-associated human diseases may help understand their function. Here we provide genetic, statistical, and clinical evidence to support association of ZNF148 with a new intellectual disability (ID) syndrome disorder. METHODS Routine diagnostic exome sequencing data were obtained from 2172 patients with ID and/or multiple congenital anomalies. RESULTS In a cohort of 2172 patient-parent trios referred for routine diagnostic whole exome sequencing for ID and/or multiple congenital anomalies (MCA) in the period 2012-2016, four patients were identified who carried de novo heterozygous nonsense or frameshift mutations in the ZNF148 gene. This was the only ZNF gene with recurrent truncating de novo mutations in this cohort. All mutations resulted in premature termination codons in the last exon of ZNF148. The number of the de novo truncating mutations in the ZNF148 gene was significantly enriched (p = 5.42 × 10-3). The newly described ZNF148-associated syndrome is characterized by underdevelopment of the corpus callosum, mild to moderate developmental delay and ID, variable microcephaly or mild macrocephaly, short stature, feeding problems, facial dysmorphisms, and cardiac and renal malformations. CONCLUSIONS We propose ZNF148 as a gene involved in a newly described ID syndrome with a recurrent phenotype and postulate that the ZNF148 is a hitherto unrecognized but crucial transcription factor in the development of the corpus callosum. Our study illustrates the advantage of whole exome sequencing in a large cohort using a parent-offspring trio approach for identifying novel genes involved in rare human diseases.
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Affiliation(s)
- Servi J C Stevens
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Conny M A van Ravenswaaij
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, The Netherlands
| | - Abdallah F Elias
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT, USA
| | - Jaclyn A Haven
- Department of Medical Genetics, Shodair Children's Hospital, Helena, MT, USA
| | - Stefan H Lelieveld
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Rolph Pfundt
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Willy M Nillesen
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Helger G Yntema
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Kees van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.,Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Alexander P Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands
| | - Christian Gilissen
- Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
| | - Han G Brunner
- Department of Clinical Genetics, Maastricht University Medical Center (MUMC+), PO Box 5800, 6202, AZ, Maastricht, The Netherlands.,Department of Genetics, Radboud University Medical Center (RUMC), Nijmegen, The Netherlands
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27
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Bie AS, Fernandez-Guerra P, Birkler RID, Nisemblat S, Pelnena D, Lu X, Deignan JL, Lee H, Dorrani N, Corydon TJ, Palmfeldt J, Bivina L, Azem A, Herman K, Bross P. Effects of a Mutation in the HSPE1 Gene Encoding the Mitochondrial Co-chaperonin HSP10 and Its Potential Association with a Neurological and Developmental Disorder. Front Mol Biosci 2016; 3:65. [PMID: 27774450 PMCID: PMC5053987 DOI: 10.3389/fmolb.2016.00065] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/21/2016] [Indexed: 11/13/2022] Open
Abstract
We here report molecular investigations of a missense mutation in the HSPE1 gene encoding the HSP10 subunit of the HSP60/ HSP10 chaperonin complex that assists protein folding in the mitochondrial matrix. The mutation was identified in an infant who came to clinical attention due to infantile spasms at 3 months of age. Clinical exome sequencing revealed heterozygosity for a HSPE1 NM_002157.2:c.217C>T de novo mutation causing replacement of leucine with phenylalanine at position 73 of the HSP10 protein. This variation has never been observed in public exome sequencing databases or the literature. To evaluate whether the mutation may be disease-associated we investigated its effects by in vitro and ex vivo studies. Our in vitro studies indicated that the purified mutant protein was functional, yet its thermal stability, spontaneous refolding propensity, and resistance to proteolytic treatment were profoundly impaired. Mass spectrometric analysis of patient fibroblasts revealed barely detectable levels of HSP10-p.Leu73Phe protein resulting in an almost 2-fold decrease of the ratio of HSP10 to HSP60 subunits. Amounts of the mitochondrial superoxide dismutase SOD2, a protein whose folding is known to strongly depend on the HSP60/HSP10 complex, were decreased to approximately 20% in patient fibroblasts in spite of unchanged SOD2 transcript levels. As a likely consequence, mitochondrial superoxide levels were increased about 2-fold. Although, we cannot exclude other causative or contributing factors, our experimental data support the notion that the HSP10-p.Leu73Phe mutation could be the cause or a strong contributing factor for the disorder in the described patient.
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Affiliation(s)
- Anne S Bie
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Paula Fernandez-Guerra
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Rune I D Birkler
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Shahar Nisemblat
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Dita Pelnena
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Xinping Lu
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Joshua L Deignan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles Los Angeles, CA, USA
| | - Hane Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los Angeles Los Angeles, CA, USA
| | - Naghmeh Dorrani
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California, Los AngelesLos Angeles, CA, USA; Department of Pediatrics, David Geffen School of Medicine at University of California, Los AngelesLos Angeles, CA, USA
| | | | - Johan Palmfeldt
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
| | - Liga Bivina
- Division of Genomic Medicine, Department of Pediatrics, UC Davis Health System Sacramento, CA, USA
| | - Abdussalam Azem
- Department of Biochemistry & Molecular Biology, Tel Aviv University Tel Aviv, Israel
| | - Kristin Herman
- Division of Genomic Medicine, Department of Pediatrics, UC Davis Health System Sacramento, CA, USA
| | - Peter Bross
- Research Unit for Molecular Medicine, Aarhus University and Aarhus University Hospital Aarhus, Denmark
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28
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Hu H, Coon H, Li M, Yandell M, Huff CD. VARPRISM: incorporating variant prioritization in tests of de novo mutation association. Genome Med 2016; 8:91. [PMID: 27562213 PMCID: PMC4997702 DOI: 10.1186/s13073-016-0341-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 08/02/2016] [Indexed: 12/18/2022] Open
Abstract
Background Patients with certain genetic diseases, such as autism spectrum disorder, have increased rates of de novo mutations within some protein-coding genes. Results We introduce the VARiant PRIoritization SuM (VARPRISM), a software package which incorporates functional variant prioritization information to improve the power to detect de novo mutations influencing disease risk. VARPRISM evaluates the consequence of any given exonic mutation on the protein sequence to estimate the likelihood that the mutation is benign or damaging and conducts a likelihood ratio test on the gene level. We analyzed the Simons Simplex Collection of 2508 parent-offspring autism trios using VARPRISM, replicating 44 genes previously implicated in autism susceptibility and identifying 20 additional candidate genes, including MYO1E, KCND3, PDCD1, DLX3, and TSPAN4 (false discovery rate < 0.3). Conclusion By incorporating functional predictions, VARPRISM improved the statistical power to identify de novo mutations increasing disease risks. VARPRISM is available at http://www.hufflab.org/software/VARPRISM. Electronic supplementary material The online version of this article (doi:10.1186/s13073-016-0341-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hao Hu
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Hilary Coon
- Department of Psychiatry, University of Utah, Salt Lake City, UT, USA
| | - Man Li
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Mark Yandell
- Department of Human Genetics and USTAR Center for Genetic Discovery, University of Utah, Salt Lake City, UT, USA
| | - Chad D Huff
- Department of Epidemiology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
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29
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Preston JL, Royall AE, Randel MA, Sikkink KL, Phillips PC, Johnson EA. High-specificity detection of rare alleles with Paired-End Low Error Sequencing (PELE-Seq). BMC Genomics 2016; 17:464. [PMID: 27301885 PMCID: PMC4908710 DOI: 10.1186/s12864-016-2669-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Accepted: 04/25/2016] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Polymorphic loci exist throughout the genomes of a population and provide the raw genetic material needed for a species to adapt to changes in the environment. The minor allele frequencies of rare Single Nucleotide Polymorphisms (SNPs) within a population have been difficult to track with Next-Generation Sequencing (NGS), due to the high error rate of standard methods such as Illumina sequencing. RESULTS We have developed a wet-lab protocol and variant-calling method that identifies both sequencing and PCR errors, called Paired-End Low Error Sequencing (PELE-Seq). To test the specificity and sensitivity of the PELE-Seq method, we sequenced control E. coli DNA libraries containing known rare alleles present at frequencies ranging from 0.2-0.4 % of the total reads. PELE-Seq had higher specificity and sensitivity than standard libraries. We then used PELE-Seq to characterize rare alleles in a Caenorhabditis remanei nematode worm population before and after laboratory adaptation, and found that minor and rare alleles can undergo large changes in frequency during lab-adaptation. CONCLUSION We have developed a method of rare allele detection that mitigates both sequencing and PCR errors, called PELE-Seq. PELE-Seq was evaluated using control E. coli populations and was then used to compare a wild C. remanei population to a lab-adapted population. The PELE-Seq method is ideal for investigating the dynamics of rare alleles in a broad range of reduced-representation sequencing methods, including targeted amplicon sequencing, RAD-Seq, ddRAD, and GBS. PELE-Seq is also well-suited for whole genome sequencing of mitochondria and viruses, and for high-throughput rare mutation screens.
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Affiliation(s)
- Jessica L Preston
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA.
| | - Ariel E Royall
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Melissa A Randel
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
| | - Kristin L Sikkink
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Patrick C Phillips
- Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, Oregon, USA
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30
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Abstract
Blind and depigmented fish belonging to the species Astyanax mexicanus are outstanding models for evolutionary genetics. During their evolution in the darkness of caves, they have undergone a number of changes at the morphological, physiological, and behavioral levels, but they can still breed with their river-dwelling conspecifics. The fertile hybrids between these two morphotypes allow forward genetic approaches, from the search of quantitative trait loci to the identification of the mutations underlying the evolution of troglomorphism. We review here the past 30years of evolutionary genetics on Astyanax: from the first crosses and the discovery of convergent evolution of different Astyanax cavefish populations to the most recent evolutionary transcriptomics and genomics studies that have provided researchers with potential candidate genes to be tested using functional genetic approaches. Although significant progress has been made and some genes have been identified, cavefish have not yet fully revealed the secret of their adaptation to the absence of light. In particular, the genetic determinism of their loss of eyes seems complex and still puzzles researchers. We also discuss future research directions, including searches for the origin of cave alleles and searches for selection genome-wide, as well as the necessary but missing information on the timing of cave colonization by surface fish.
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Affiliation(s)
- D Casane
- Laboratory EGCE, CNRS and University of Paris-Sud, Gif-sur-Yvette, France; Paris Diderot University, Sorbonne Paris Cité, France
| | - S Rétaux
- Paris-Saclay Institute of Neuroscience, CNRS and University Paris-Sud, Gif-sur-Yvette, France
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31
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Erickson RP. The importance of de novo mutations for pediatric neurological disease--It is not all in utero or birth trauma. Mutat Res Rev Mutat Res 2016; 767:42-58. [PMID: 27036065 DOI: 10.1016/j.mrrev.2015.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 12/23/2015] [Accepted: 12/23/2015] [Indexed: 01/30/2023]
Abstract
The advent of next generation sequencing (NGS, which consists of massively parallel sequencing to perform TGS (total genome sequencing) or WES (whole exome sequencing)) has abundantly discovered many causative mutations in patients with pediatric neurological disease. A surprisingly high number of these are de novo mutations which have not been inherited from either parent. For epilepsy, autism spectrum disorders, and neuromotor disorders, including cerebral palsy, initial estimates put the frequency of causative de novo mutations at about 15% and about 10% of these are somatic. There are some shared mutated genes between these three classes of disease. Studies of copy number variation by comparative genomic hybridization (CGH) proceded the NGS approaches but they also detect de novo variation which is especially important for ASDs. There are interesting differences between the mutated genes detected by CGS and NGS. In summary, de novo mutations cause a very significant proportion of pediatric neurological disease.
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Affiliation(s)
- Robert P Erickson
- Dept. of Pediatrics, University of Arizona College of Medicine, Tucson, AZ 85724, United States.
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Grattan RE, Morton SE, Warhurst ES, Parker TR, Nicolson MP, Maha JLK, Linscott RJ. Paternal and maternal ages have contrasting associations with self-reported schizophrenia liability. Schizophr Res 2015; 169:308-312. [PMID: 26421690 DOI: 10.1016/j.schres.2015.09.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 09/15/2015] [Indexed: 01/06/2023]
Abstract
BACKGROUND Older paternal age predicts schizophrenia diagnosis in offspring. If this relationship reflects a pathogenic process, paternal age should predict the expression of subclinical schizophrenia liability (schizotypy). We hypothesized that paternal and maternal ages predict positive, negative, and disorganized features of schizotypy, that family history of psychosis moderates the relationship of paternal age with schizotypy, and that stress sensitivity mediates the relationship of maternal age with schizotypy. METHOD Two studies are reported, each of undergraduates (n=500 and n=211) who completed the Schizotypal Personality Questionnaire. The second was designed to replicate and extend the first and included assessment of stress sensitivity. RESULTS In Study 1, older paternal age and younger maternal age predicted greater positive schizotypy (β=.13 and β=-.19, respectively). Parental ages did not predict negative or disorganized features and family history did not moderate the paternal age association. In Study 2, the same pattern of associations between parental ages and schizotypy components was observed. Additionally, stress sensitivity partially mediated the association of maternal age with positive schizotypy whereas it did not contribute to the paternal age association. CONCLUSION The association between older paternal age and schizophrenia extends to self-reported positive features of schizophrenia liability, consistent with the notion that this relationship arises from a pathogenic process, such as de novo mutations. Importantly, younger maternal age was an equally potent predictor of positive schizotypy, with its association partially mediated by stress sensitivity.
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Affiliation(s)
| | - Sarah E Morton
- Department of Psychology, University of Otago, New Zealand
| | | | | | - Max P Nicolson
- Department of Psychology, University of Otago, New Zealand
| | | | - Richard J Linscott
- Department of Psychology, University of Otago, New Zealand; Department of Psychiatry and Psychology, Maastricht University, Maastricht, The Netherlands.
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Shang L, Henderson LB, Cho MT, Petrey DS, Fong CT, Haude KM, Shur N, Lundberg J, Hauser N, Carmichael J, Innis J, Schuette J, Wu YW, Asaikar S, Pearson M, Folk L, Retterer K, Monaghan KG, Chung WK. De novo missense variants in PPP2R5D are associated with intellectual disability, macrocephaly, hypotonia, and autism. Neurogenetics 2015; 17:43-9. [PMID: 26576547 DOI: 10.1007/s10048-015-0466-9] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 10/22/2015] [Indexed: 12/19/2022]
Abstract
Protein phosphatase 2A (PP2A) is a heterotrimeric protein serine/threonine phosphatase and is involved in a broad range of cellular processes. PPP2R5D is a regulatory B subunit of PP2A and plays an important role in regulating key neuronal and developmental regulation processes such as PI3K/AKT and glycogen synthase kinase 3 beta (GSK3β)-mediated cell growth, chromatin remodeling, and gene transcriptional regulation. Using whole-exome sequencing (WES), we identified four de novo variants in PPP2R5D in a total of seven unrelated individuals with intellectual disability (ID) and other shared clinical characteristics, including autism spectrum disorder, macrocephaly, hypotonia, seizures, and dysmorphic features. Among the four variants, two have been previously reported and two are novel. All four amino acids are highly conserved among the PP2A subunit family, and all change a negatively charged acidic glutamic acid (E) to a positively charged basic lysine (K) and are predicted to disrupt the PP2A subunit binding and impair the dephosphorylation capacity. Our data provides further support for PPP2R5D as a genetic cause of ID.
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Affiliation(s)
- Linshan Shang
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | | | | | - Donald S Petrey
- Department of Biochemistry and Molecular Biophysics, Columbia University Medical Center, New York, NY, USA
| | - Chin-To Fong
- University of Rochester Medical Center, Rochester, NY, USA
| | | | | | | | | | | | - Jeffrey Innis
- Division of Pediatric Genetics, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jane Schuette
- Division of Pediatric Genetics, University of Michigan Health System, Ann Arbor, MI, USA
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Yvonne W Wu
- Departments of Neurology and Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.
- Department of Medicine, Columbia University Medical Center, New York, NY, USA.
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Schmeidler J, Lazzeroni LC, Swerdlow NR, Ferreira RP, Braff DL, Calkins ME, Cadenhead KS, Freedman R, Green MF, Greenwood TA, Gur RE, Gur RC, Light GA, Olincy A, Nuechterlein KH, Radant AD, Seidman LJ, Siever LJ, Stone WS, Sprock J, Sugar CA, Tsuang DW, Tsuang MT, Turetsky BI, Silverman JM. Paternal age of schizophrenia probands and endophenotypic differences from unaffected siblings. Psychiatry Res 2014; 219:67-71. [PMID: 24913833 PMCID: PMC4110721 DOI: 10.1016/j.psychres.2014.05.035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 02/07/2014] [Accepted: 05/18/2014] [Indexed: 01/06/2023]
Abstract
We evaluated the discrepancy of endophenotypic performance between probands with schizophrenia and unaffected siblings by paternal age at proband birth, a possible marker for de novo mutations. Pairs of schizophrenia probands and unaffected siblings (N=220 pairs) were evaluated on 11 neuropsychological or neurophysiological endophenotypes previously identified as heritable. For each endophenotype, the sibling-minus-proband differences were transformed to standardized scores. Then for each pair, the average discrepancy was calculated from its standardized scores. We tested the hypothesis that the discrepancy is associated with paternal age, controlling for the number of endophenotypes shared between proband and his or her sibling, and proband age, which were both associated with paternal age. The non-significant association between the discrepancy and paternal age was in the opposite direction from the hypothesis. Of the 11 endophenotypes only sensori-motor dexterity was significant, but in the opposite direction. Eight other endophenotypes were also in the opposite direction, but not significant. The results did not support the hypothesized association of increased differences between sibling/proband pairs with greater paternal age. A possible explanation is that the identification of heritable endophenotypes was based on samples for which schizophrenia was attributable to inherited rather than de novo/non-inherited causes.
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Affiliation(s)
- James Schmeidler
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai School, One Gustave L. Levy Place, Box 1230, New York, NY, USA
| | - Laura C Lazzeroni
- Department of Psychiatry and Behavioral Sciences, Stanford University, Palo Alto, CA, USA
| | - Neal R Swerdlow
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Rui P Ferreira
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai School, One Gustave L. Levy Place, Box 1230, New York, NY, USA
| | - David L Braff
- Department of Psychiatry, University of California, San Diego, CA, USA; VISN-22 Mental Illness Research, Education, and Clinical Center, VA San Diego Healthcare System, San Diego, CA, USA
| | - Monica E Calkins
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Robert Freedman
- Department of Psychiatry, University of Colorado Health Sciences Center, Denver, CO, USA
| | - Michael F Green
- Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine at University of California, Los Angeles, CA, USA; VA Greater Los Angeles Health Care System, Los Angeles, CA, USA
| | | | - Raquel E Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Ruben C Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Gregory A Light
- Department of Psychiatry, University of California, San Diego, CA, USA; VISN-22 Mental Illness Research, Education, and Clinical Center, VA San Diego Healthcare System, San Diego, CA, USA
| | - Ann Olincy
- Department of Psychiatry, University of Colorado Health Sciences Center, Denver, CO, USA
| | - Keith H Nuechterlein
- Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine at University of California, Los Angeles, CA, USA
| | - Allen D Radant
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA
| | - Larry J Seidman
- Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Harvard Medical School Department of Psychiatry, Boston, MA, USA
| | - Larry J Siever
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai School, One Gustave L. Levy Place, Box 1230, New York, NY, USA; VISN-3 Mental Illness Research, Education, and Clinical Center, James J. Peters VA Medical Center, New York, NY, USA
| | - William S Stone
- Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Harvard Medical School Department of Psychiatry, Boston, MA, USA
| | - Joyce Sprock
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Catherine A Sugar
- Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine at University of California, Los Angeles, CA, USA; VA Greater Los Angeles Health Care System, Los Angeles, CA, USA
| | - Debby W Tsuang
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, USA; VISN-20 Geriatric Research, Education, and Clinical Center, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Ming T Tsuang
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Bruce I Turetsky
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
| | - Jeremy M Silverman
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai School, One Gustave L. Levy Place, Box 1230, New York, NY, USA; James J. Peters Veterans Affairs Medical Center, Bronx, NY 10468, USA.
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