1
|
Gunasekaran ND, Jayasankaran C, Justin Margret J, Krishnamoorthy M, Srisailapathy CRS. Evaluation of recurrent GNPTAB, GNPTG, and NAGPA variants associated with stuttering. ADVANCED GENETICS (HOBOKEN, N.J.) 2021; 2:e10043. [PMID: 36618124 PMCID: PMC9744500 DOI: 10.1002/ggn2.10043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 01/11/2023]
Abstract
Stuttering is a childhood-onset fluency disorder, intertwined with physiological, emotional, and anxiety factors. The present study was designed to evaluate the recurrence of the reported mutations among three previously implicated (GNPTAB, GNPTG, NAGPA) candidate genes, in persons with stuttering from south India. Mutation screening was performed among 64 probands on 12 specific exons, by Sanger sequencing. A total of 12 variants were identified, which included five nonsynonymous, five synonymous, and two noncoding variants. Three unrelated probands harbored heterozygous missense variants at conserved coding positions across species (p. Glu1200Lys in GNPTAB, p. Ile268Leu in GNPTG and p. Arg44Pro in NAGPA). Of these, only one variant (p. Glu1200Lys in GNPTAB) cosegregated with the affected status while p. Ile268Leu in GNPTG gene was found to be a rare de novo variant. Although this study identified some previously reported variants that have been claimed to have a role in stuttering, we confirmed only one of these to be a likely causal de novo variant (p.Ile268Leu) in the GNPTG gene at an allele frequency of 0.8% (1/128) in the families with stuttering.
Collapse
Affiliation(s)
- Nandhini Devi Gunasekaran
- Department of Genetics, Post Graduate Institute of Basic Medical SciencesUniversity of Madras, Taramani CampusChennaiIndia
| | - Chandru Jayasankaran
- Department of Genetics, Post Graduate Institute of Basic Medical SciencesUniversity of Madras, Taramani CampusChennaiIndia,LifeBytes India Pvt. LtdBengaluruKarnatakaIndia
| | - Jeffrey Justin Margret
- Department of Genetics, Post Graduate Institute of Basic Medical SciencesUniversity of Madras, Taramani CampusChennaiIndia
| | - Mathuravalli Krishnamoorthy
- Department of Genetics, Post Graduate Institute of Basic Medical SciencesUniversity of Madras, Taramani CampusChennaiIndia
| | - C. R. Srikumari Srisailapathy
- Department of Genetics, Post Graduate Institute of Basic Medical SciencesUniversity of Madras, Taramani CampusChennaiIndia
| |
Collapse
|
2
|
Liu Y, Zheng Z, Zhu Q. Case Report: Identification of Polygenic Mutations by Exome Sequencing. Front Pediatr 2021; 9:689901. [PMID: 34746046 PMCID: PMC8567987 DOI: 10.3389/fped.2021.689901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 09/09/2021] [Indexed: 11/18/2022] Open
Abstract
The discovery of rare genetic variation through different gene sequencing methods is a very challenging subject in the field of human genetics. A case of a 1-year-old boy with metabolic acidosis and hypokalemia, a small penis, growth retardation, and G-6PD deficiency was reported. Since the clinical symptoms are complex and seem uncorrelated, the authors hypothesized that the child had chromosome or gene problems, and exome sequencing (ES) was applied to samples from him and his parents. Three main locus mutations in three genes were found in the proband, including SLC4A1, FGFR1, and G6PD genes. A missense mutation (c.1766G>T, p.R589 L) was found in exon 14 of SLC4A1 gene, which was a de novo mutation. Another missense mutation (c.1028 A>G, p.H343R) was found in exon 9 of FGFR1 gene, which was also a de novo mutation. These findings further demonstrate the utility of ES in the diagnosis of rare diseases.
Collapse
Affiliation(s)
- Yanfeng Liu
- Department of Endocrinology, Quanzhou Women and Children's Hospital, Quanzhou, China
| | - Zhongshi Zheng
- Department of Endocrinology, Quanzhou Women and Children's Hospital, Quanzhou, China
| | - Qingling Zhu
- Department of Children Health Care, Quanzhou Women and Children's Hospital, Quanzhou, China
| |
Collapse
|
3
|
Hoehe MR, Herwig R, Mao Q, Peters BA, Drmanac R, Church GM, Huebsch T. Significant abundance of cis configurations of coding variants in diploid human genomes. Nucleic Acids Res 2019; 47:2981-2995. [PMID: 30698752 PMCID: PMC6451136 DOI: 10.1093/nar/gkz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 12/05/2018] [Accepted: 01/15/2019] [Indexed: 12/12/2022] Open
Abstract
To fully understand human genetic variation and its functional consequences, the specific distribution of variants between the two chromosomal homologues of genes must be known. The 'phase' of variants can significantly impact gene function and phenotype. To assess patterns of phase at large scale, we have analyzed 18 121 autosomal genes in 1092 statistically phased genomes from the 1000 Genomes Project and 184 experimentally phased genomes from the Personal Genome Project. Here we show that genes with cis-configurations of coding variants are more frequent than genes with trans-configurations in a genome, with global cis/trans ratios of ∼60:40. Significant cis-abundance was observed in virtually all genomes in all populations. Moreover, we identified a large group of genes exhibiting cis-configurations of protein-changing variants in excess, so-called 'cis-abundant genes', and a smaller group of 'trans-abundant genes'. These two gene categories were functionally distinguishable, and exhibited strikingly different distributional patterns of protein-changing variants. Underlying these phenomena was a shared set of phase-sensitive genes of importance for adaptation and evolution. This work establishes common patterns of phase as key characteristics of diploid human exomes and provides evidence for their functional significance, highlighting the importance of phase for the interpretation of protein-coding genetic variation and gene function.
Collapse
Affiliation(s)
- Margret R Hoehe
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Ralf Herwig
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| | - Qing Mao
- Complete Genomics, Inc., San Jose, CA 95112, USA
| | - Brock A Peters
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - Radoje Drmanac
- Complete Genomics, Inc., San Jose, CA 95112, USA.,BGI-Shenzhen, Shenzhen 518083, China
| | - George M Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Thomas Huebsch
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
| |
Collapse
|
4
|
Hu Z, Yu C, Furutsuki M, Andreoletti G, Ly M, Hoskins R, Adhikari AN, Brenner SE. VIPdb, a genetic Variant Impact Predictor Database. Hum Mutat 2019; 40:1202-1214. [PMID: 31283070 PMCID: PMC7288905 DOI: 10.1002/humu.23858] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 06/27/2019] [Indexed: 12/30/2022]
Abstract
Genome sequencing identifies vast number of genetic variants. Predicting these variants' molecular and clinical effects is one of the preeminent challenges in human genetics. Accurate prediction of the impact of genetic variants improves our understanding of how genetic information is conveyed to molecular and cellular functions, and is an essential step towards precision medicine. Over one hundred tools/resources have been developed specifically for this purpose. We summarize these tools as well as their characteristics, in the genetic Variant Impact Predictor Database (VIPdb). This database will help researchers and clinicians explore appropriate tools, and inform the development of improved methods. VIPdb can be browsed and downloaded at https://genomeinterpretation.org/vipdb.
Collapse
Affiliation(s)
- Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Changhua Yu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Mabel Furutsuki
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Department of Electrical Engineering and Computer Sciences, University of California, Berkeley, California 94720, USA
| | - Gaia Andreoletti
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Melissa Ly
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Division of Data Sciences, University of California, Berkeley, California 94720, USA
| | - Roger Hoskins
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Aashish N. Adhikari
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Steven E. Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| |
Collapse
|
5
|
Khan R, Aftab A, Tabassum S, Hussain HMJ, Hameed A, Mahmood H, Munir F, Bukhari I. Identification of CDKN2A variants in breast cancer patients in Pakistan. Genes Genet Syst 2019; 94:117-122. [PMID: 31231091 DOI: 10.1266/ggs.18-00053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The role of cyclin-dependent kinase inhibitor 2A gene (CDKN2A) variants in breast cancer is not well understood, here we investigated their possible effects on breast cancer in Pakistani women attending the NORI Hospital, Islamabad. Direct DNA sequencing of CDKN2A identified an already known polymorphism in the 3' UTR, c.*29G>C (rs11515), in 5.88% patients and two novel variants. One, a deep intronic substitution (c.458-554T>G) in 1.96% patients, is also detected as a compound heterozygous form along with c.*29G>C in 1.96% patients (c.[458-554T>G; *29G>C]). The other is a novel deletion (c.458-82delG) occurring as a compound variant with two other identified variants c.[458-554T>G; 458-82delG; *29G>C] in 1.96% patients. In silico pathogenicity prediction analyses did not predict pathogenic effects on breast cancer for these individual variants. We conclude that variations in CDKN2A are not the major genetic cause of breast cancer in the enrolled Pakistani patients.
Collapse
Affiliation(s)
- Ranjha Khan
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China
| | - Ayesha Aftab
- Department of Biological Sciences, International Islamic University
| | - Sobia Tabassum
- Department of Biological Sciences, International Islamic University
| | - Hafiz Muhammad Jafar Hussain
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China
| | - Abdul Hameed
- Institute of Biomedical and Genetic Engineering (IBGE)
| | - Humera Mahmood
- Department of Oncology, Nuclear Medicine Oncology & Radiotherapy Institute (NORI) Hospital
| | - Faiza Munir
- Department of Biological Sciences, International Islamic University
| | - Ihtisham Bukhari
- Translational Research Institute, Henan Provincial People's Hospital, School of Medicine, Henan University
| |
Collapse
|
6
|
Buckley AR, Ideker T, Carter H, Schork NJ. Rare variant phasing using paired tumor:normal sequence data. BMC Bioinformatics 2019; 20:265. [PMID: 31132991 PMCID: PMC6537421 DOI: 10.1186/s12859-019-2753-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 03/19/2019] [Indexed: 01/08/2023] Open
Abstract
Background In standard high throughput sequencing analysis, genetic variants are not assigned to a homologous chromosome of origin. This process, called haplotype phasing, can reveal information important for understanding the relationship between genetic variants and biological phenotypes. For example, in genes that carry multiple heterozygous missense variants, phasing resolves whether one or both gene copies are altered. Here, we present a novel approach to phasing variants that takes advantage of unique properties of paired tumor:normal sequencing data from cancer studies. Results VAF phasing uses changes in variant allele frequency (VAF) between tumor and normal samples in regions of somatic chromosomal gain or loss to phase germline variants. We apply VAF phasing to 6180 samples from the Cancer Genome Atlas (TCGA) and demonstrate that our method is highly concordant with other standard phasing methods, and can phase an average of 33% more variants than other read-backed phasing methods. Using variant annotation tools designed to score gene haplotypes, we find a suggestive association between carrying multiple missense variants in a single copy of a cancer predisposition gene and earlier age of cancer diagnosis. Conclusions VAF phasing exploits unique properties of tumor genomes to increase the number of germline variants that can be phased over standard read-backed methods in paired tumor:normal samples. Our phase-informed association testing results call attention to the need to develop more tools for assessing the joint effect of multiple genetic variants. Electronic supplementary material The online version of this article (10.1186/s12859-019-2753-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Alexandra R Buckley
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA.,Human Biology Program, J. Craig Venter Institute, La Jolla, CA, USA
| | - Trey Ideker
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA, USA
| | - Hannah Carter
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.,Cancer Cell Map Initiative (CCMI), University of California San Diego, La Jolla, CA, USA
| | - Nicholas J Schork
- Human Biology Program, J. Craig Venter Institute, La Jolla, CA, USA. .,Department of Quantitative Medicine and Systems Biology, The Translational Genomics Research Institute, Phoenix, AZ, USA. .,Departments of Family Medicine and Public Health and Psychiatry, University of California San Diego, La Jolla, CA, USA.
| |
Collapse
|
7
|
Piotrowska-Nowak A, Kosior-Jarecka E, Schab A, Wrobel-Dudzinska D, Bartnik E, Zarnowski T, Tonska K. Investigation of whole mitochondrial genome variation in normal tension glaucoma. Exp Eye Res 2018; 178:186-197. [PMID: 30312593 DOI: 10.1016/j.exer.2018.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/16/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023]
Abstract
Glaucoma is one of the leading causes of visual impairment and blindness worldwide. However, the cause of retinal ganglion cell loss and damage of the optic nerve in its pathogenesis is largely unknown. The high energy demands of these cells may reflect their strong dependence on mitochondrial function and thus sensitivity to mitochondrial defects. To address this issue, we studied whole mitochondrial genome variation in normal tension glaucoma patients and control individuals from the Polish population using next generation sequencing. Our findings indicate that few features of mitochondrial DNA variation are different for glaucoma patients and control subjects. New insights into normal tension glaucoma development are discussed. We provide also a comprehensive approach for mitochondrial DNA analysis and variant evaluation.
Collapse
Affiliation(s)
- Agnieszka Piotrowska-Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Aleksandra Schab
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Dominika Wrobel-Dudzinska
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland; Institute of Biochemistry and Biophysics Polish Academy of Sciences, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| | - Tomasz Zarnowski
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, Chmielna 1 Street, Lublin, 20-079, Poland.
| | - Katarzyna Tonska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Pawinskiego 5a Street, Warsaw, 02-106, Poland.
| |
Collapse
|
8
|
Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA. Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel. Front Cell Infect Microbiol 2018; 8:193. [PMID: 29971217 PMCID: PMC6018220 DOI: 10.3389/fcimb.2018.00193] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 05/22/2018] [Indexed: 12/30/2022] Open
Abstract
Leptospirosis is a worldwide zoonosis, responsible for more than 1 million cases and 60,000 deaths every year. Among the 13 pathogenic species of the genus Leptospira, serovars belonging to L. interrogans serogroup Icterohaemorrhagiae are considered to be the most virulent strains, and responsible for majority of the reported severe cases. Serovars Copenhageni and Icterohaemorrhagiae are major representatives of this serogroup and despite their public health relevance, little is known regarding the genetic differences between these two serovars. In this study, we analyzed the genome sequences of 67 isolates belonging to L. interrogans serovars Copenhageni and Icterohaemorrhagiae to investigate the influence of spatial and temporal variations on DNA sequence diversity. Out of the 1072 SNPs identified, 276 were in non-coding regions and 796 in coding regions. Indel analyses identified 258 indels, out of which 191 were found in coding regions and 67 in non-coding regions. Our phylogenetic analyses based on SNP dataset revealed that both serovars are closely related but showed distinct spatial clustering. However, likelihood ratio test of the indel data statistically confirmed the presence of a frameshift mutation within a homopolymeric tract of lic12008 gene (related to LPS biosynthesis) in all the L. interrogans serovar Icterohaemorrhagiae strains but not in the Copenhageni strains. Therefore, this internal indel identified can genetically distinguish L. interrogans serovar Copenhageni from serovar Icterohaemorrhagiae with high discriminatory power. To our knowledge, this is the first study to identify global sequence variations (SNPs and Indels) in L. interrogans serovars Copenhageni and Icterohaemorrhagiae.
Collapse
Affiliation(s)
- Luciane A Santos
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.,Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Haritha Adhikarla
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States
| | - Xiting Yan
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Zheng Wang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | | | - Joseph M Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, CA, United States
| | | | - Rudy A Hartskeerl
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, Netherlands
| | - Marga G A Goris
- Royal Tropical Institute, KIT Biomedical Research, Amsterdam, Netherlands
| | | | | | - Jeffrey P Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Hongyu Zhao
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, United States
| | - Albert I Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.,Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| | - Elsio A Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, United States.,Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Brazil
| |
Collapse
|
9
|
What Does This Mutation Mean? The Tools and Pitfalls of Variant Interpretation in Lymphoid Malignancies. Int J Mol Sci 2018; 19:ijms19041251. [PMID: 29677173 PMCID: PMC5979354 DOI: 10.3390/ijms19041251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 04/09/2018] [Accepted: 04/14/2018] [Indexed: 01/21/2023] Open
Abstract
High throughput sequencing (HTS) is increasingly important in determining cancer diagnoses, with subsequent prognostic and therapeutic implications. The biology of cancer is becoming increasingly deciphered and it is clear that therapy needs to be individually tailored. Whilst translational research plays an important role in lymphoid malignancies, few guidelines exist to guide biologists and routine laboratories through this constantly evolving field. In this article, we review the challenges of interpreting HTS in lymphoid malignancies and provide a toolkit to interpret single nucleotide variants obtained from HTS. We define the pre-analytical issues such as sequencing DNA obtained from formalin-fixed and paraffin-embedded tissue (FFPE), the acquisition of germline DNA, or the bioinformatic pitfalls, the analytical issues encountered and how to manage them. We describe the main constitutional and cancer databases, their characteristics and limitations, with an emphasis on variant interpretation in lymphoid malignancies. Finally, we discuss the challenges of predictions that one can make using in silico or in vitro modelling, pharmacogenomic screening, and the limits of those prediction tools. This description of the current status in genomic interpretation highlights the need for new large databases and international collaboration in the lymphoma field.
Collapse
|
10
|
Lauschke VM, Ingelman-Sundberg M. Requirements for comprehensive pharmacogenetic genotyping platforms. Pharmacogenomics 2016; 17:917-24. [PMID: 27248710 DOI: 10.2217/pgs-2016-0023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Recent research highlighted the large extent of rare variants in pharmacogenes and, on this basis, it was estimated that rare variants account for 30-40% of the functional variability in pharmacogenes. It has been proposed that comprehensive next-generation sequencing (NGS)-based sequencing of pharmacogenes could soon be a cost-effective methodology for clinical routine genotyping. Yet, multiple challenges on technical, interpretative and ethical levels need to be overcome to enable the reasonable dissemination of comprehensive pharmacogenetic genotyping, that includes rare genetic variation, into clinical practice. We argue that current pre-emptive pharmacogenetic testing cannot be based on comprehensive approaches but needs to be restricted to validated variants. Rather, comprehensive strategies should only be used for retrospective analyses of patients exhibiting unanticipated drug responses. Thereby, subsequent to computational analyses and functional validations, emerging variants with confirmed functional relevance can be incorporated into candidate genotyping strategies, thus refining and enhancing future pre-emptive genetic testing.
Collapse
Affiliation(s)
- Volker M Lauschke
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| | - Magnus Ingelman-Sundberg
- Section of Pharmacogenetics, Department of Physiology & Pharmacology, Karolinska Institutet, SE-17177 Stockholm, Sweden
| |
Collapse
|