1
|
Jepsen AH, Kampmann ML, Jacobsen SB, Børsting C, Andersen JD. Identification of individuals from low template blood samples using whole transcriptome shotgun sequencing. Forensic Sci Int Genet 2024; 72:103089. [PMID: 38905753 DOI: 10.1016/j.fsigen.2024.103089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 06/14/2024] [Accepted: 06/19/2024] [Indexed: 06/23/2024]
Abstract
Biological trace samples consisting of very few cells pose a challenge to conventional forensic genetic DNA analysis. RNA may be an alternative to DNA when handling low template samples. Whereas each cell only contains two copies of an autosomal DNA segment, the transcriptome retains much of the genomic variation replicated in abundant RNA fragments. In this study, we describe the development of a prototype RNA-based SNP selection set for forensic human identification from low template samples (50 pg gDNA). Whole blood from a subset of the Danish population (41 individuals) and blood stains subjected to degradation at room temperature for up to two weeks were analysed by whole transcriptome shotgun sequencing. Concordance was determined by DNA genotyping with the Infinium Omni5-4 SNP chip. In the 100 protein-coding genes with the most reads, 5214 bi-allelic SNPs with gnomAD minor allele frequencies > 0.1 in the African/African American, East Asian, and (non-Finnish) European populations were identified. Of these, 24 SNPs in 21 genes passed screening in whole blood and degraded blood stains, with a resulting mean match probability of 4.5 ∙ 10-9. Additionally, ancestry informative SNPs and SNPs in genes useful for body fluid identification were identified in the transcriptome. Consequently, shotgun sequencing of RNA from low template samples may be used for a vast host of forensic genetics purposes, including simultaneous human and body fluid identification, leading to direct donor identification in the identified body fluid.
Collapse
Affiliation(s)
- Alberte Honoré Jepsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark.
| | - Marie-Louise Kampmann
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark
| | - Stine Bøttcher Jacobsen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark
| | - Claus Børsting
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark
| | - Jeppe Dyrberg Andersen
- Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Frederik V's Vej 11, Copenhagen DK-2100, Denmark
| |
Collapse
|
2
|
Hu J, Korchina V, Zouk H, Harden MV, Murdock D, Macbeth A, Harrison SM, Lennon N, Kovar C, Balasubramanian A, Zhang L, Chandanavelli G, Pasham D, Rowley R, Wiley K, Smith ME, Gordon A, Jarvik GP, Sleiman P, Kelly MA, Bland HT, Murugan M, Venner E, Boerwinkle E, Prows C, Mahanta L, Rehm HL, Gibbs RA, Muzny DM. Genetic sex validation for sample tracking in next-generation sequencing clinical testing. BMC Res Notes 2024; 17:62. [PMID: 38433186 PMCID: PMC10910835 DOI: 10.1186/s13104-024-06723-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024] Open
Abstract
OBJECTIVE Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. RESULTS Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors (49.09%), samples from transgender participants (3.64%) and stem cell or bone marrow transplant patients (7.27%) along with undetermined sample mix-ups (40%) for which sample swaps occurred prior to arrival at genome centers, however the exact cause of the events at the sampling sites resulting in the mix-ups were not able to be determined.
Collapse
Affiliation(s)
- Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Viktoriya Korchina
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Hana Zouk
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | | | - David Murdock
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Steven M Harrison
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Niall Lennon
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Christie Kovar
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | | | - Lan Zhang
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | | | - Divya Pasham
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Robb Rowley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Ken Wiley
- Division of Genomic Medicine, National Human Genome Research Institute, Bethesda, MD, USA
| | - Maureen E Smith
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Adam Gordon
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Patrick Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Harris T Bland
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - Mullai Murugan
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Eric Venner
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Eric Boerwinkle
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
- Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Cynthia Prows
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Lisa Mahanta
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
| | - Heidi L Rehm
- Laboratory for Molecular Medicine (LMM), Mass General Brigham, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Richard A Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA
| | - Donna M Muzny
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC), Houston, TX, USA.
| |
Collapse
|
3
|
Ve K, R R, Cac P, A K, E T, Cc S, Ab O. Single Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting (SNACS): A tool for demultiplexing single-cell DNA sequencing data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.07.579345. [PMID: 38370638 PMCID: PMC10871358 DOI: 10.1101/2024.02.07.579345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
Motivation Recently, single-cell DNA sequencing (scDNA-seq) and multi-modal profiling with the addition of cell-surface antibodies (scDAb-seq) have provided key insights into cancer heterogeneity. Scaling these technologies across large patient cohorts, however, is cost and time prohibitive. Multiplexing, in which cells from unique patients are pooled into a single experiment, offers a possible solution. While multiplexing methods exist for scRNAseq, accurate demultiplexing in scDNAseq remains an unmet need. Results Here, we introduce SNACS: Single-Nucleotide Polymorphism (SNP) and Antibody-based Cell Sorting. SNACS relies on a combination of patient-level cell-surface identifiers and natural variation in genetic polymorphisms to demultiplex scDNAseq data. We demonstrated the performance of SNACS on a dataset consisting of multi-sample experiments from patients with leukemia where we knew truth from single-sample experiments from the same patients. Using SNACS, accuracy ranged from 0.948 - 0.991 vs 0.552 - 0.934 using demultiplexing methods from the single-cell literature.
Collapse
Affiliation(s)
- Kennedy Ve
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Roy R
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Peretz Cac
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Division of Hematology and Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Koh A
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Tran E
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Smith Cc
- Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA, 94143
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
| | - Olshen Ab
- Hellen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA, 94143
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA, 94143
| |
Collapse
|
4
|
Nguyen L. RNA therapeutics for neurological disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 203:165-180. [PMID: 38359997 DOI: 10.1016/bs.pmbts.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
Neurological disorders are the group of diseases that primarily affect the center nervous system, which could lead to a significant negative impact on the ability of learning new skills, speaking, breathing, walking, judging, making decision, and other essential living skills. In the last decade, neurological disorders have significantly increased their impact to our community and become the one of leading causes of disability and death. The World Health Organization has identified neurological disorders including Alzheimer's disease and other dementia as the health crisis for the modern life. Tremendous ongoing research efforts focus on understanding of disease genetics, molecular mechanisms and developing therapeutic interventions. Because of the urgent need of the effective therapeutics and the recent advances in the toolkits and understanding for developing more drug-like RNA molecules, there is a growing interest for developing RNA therapeutics for neurological disorders. This article will discuss genetics and mechanisms of neurological disorders and how RNA-based molecules have been used to develop therapeutics for this group of diseases, challenges of RNA therapeutics and future perspectives on this rising therapeutic intervention tool.
Collapse
Affiliation(s)
- Lien Nguyen
- Department of Molecular Genetics and Microbiology, Center for NeuroGenetics, University of Florida, Cancer Genetics Research Complex (CGRC), Gainesville, FL, United States.
| |
Collapse
|
5
|
Al-Eitan LN, ElMotasem MFM, Khair IY, Alahmad SZ. Vaccinomics: Paving the Way for Personalized Immunization. Curr Pharm Des 2024; 30:1031-1047. [PMID: 38898820 DOI: 10.2174/0113816128280417231204085137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/15/2023] [Indexed: 06/21/2024]
Abstract
Vaccines are one of the most important medical advancements in human history. They have been successfully used to control and limit the spread of many of the lethal diseases that have plagued us, such as smallpox and polio. Previous vaccine design methodologies were based on the model of "isolate-inactivateinject", which amounts to giving the same vaccine dose to everyone susceptible to infection. In recent years, the importance of how the host genetic background alters vaccine response necessitated the introduction of vaccinomics, which is aimed at studying the variability of vaccine efficacy by associating genetic variability and immune response to vaccination. Despite the rapid developments in variant screening, data obtained from association studies is often inconclusive and cannot be used to guide the new generation of vaccines. This review aims to compile the polymorphisms in HLA and immune system genes and examine the link with their immune response to vaccination. The compiled data can be used to guide the development of new strategies for vaccination for vulnerable groups. Overall, the highly polymorphic HLA locus had the highest correlation with vaccine response variability for most of the studied vaccines, and it was linked to variation in multiple stages of the immune response to the vaccines for both humoral and cellular immunity. Designing new vaccine technologies and immunization regiments to accommodate for this variability is an important step for reaching a vaccinomics-based approach to vaccination.
Collapse
Affiliation(s)
- Laith Naser Al-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Moh'd Fahmi Munib ElMotasem
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Iliya Yacoub Khair
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| | - Saif Zuhair Alahmad
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan
| |
Collapse
|
6
|
Hu J, Korchina V, Zouk H, Harden MV, Murdock D, Macbeth A, Harrison SM, Lennon N, Kovar C, Balasubramanian A, Zhang L, Chandanavelli G, Pasham D, Rowley R, Wiley K, Smith ME, Gordon A, Jarvik GP, Sleiman P, Kelly MA, Bland HT, Murugan M, Venner E, Boerwinkle E, Prows C, Mahanta L, Rehm HL, Gibbs RA, Muzny DM. Genetic Sex Validation for Sample Tracking in Clinical Testing. RESEARCH SQUARE 2023:rs.3.rs-3304685. [PMID: 37790445 PMCID: PMC10543510 DOI: 10.21203/rs.3.rs-3304685/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Objective Data from DNA genotyping via a 96-SNP panel in a study of 25,015 clinical samples were utilized for quality control and tracking of sample identity in a clinical sequencing network. The study aimed to demonstrate the value of both the precise SNP tracking and the utility of the panel for predicting the sex-by-genotype of the participants, to identify possible sample mix-ups. Results Precise SNP tracking showed no sample swap errors within the clinical testing laboratories. In contrast, when comparing predicted sex-by-genotype to the provided sex on the test requisition, we identified 110 inconsistencies from 25,015 clinical samples (0.44%), that had occurred during sample collection or accessioning. The genetic sex predictions were confirmed using additional SNP sites in the sequencing data or high-density genotyping arrays. It was determined that discrepancies resulted from clerical errors, samples from transgender participants and stem cell or bone marrow transplant patients along with undetermined sample mix-ups.
Collapse
Affiliation(s)
- Jianhong Hu
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | - Hana Zouk
- Laboratory for Molecular Medicine (LMM), Mass General Brigham
| | | | - David Murdock
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | | | | | - Christie Kovar
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | - Lan Zhang
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | - Divya Pasham
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | - Ken Wiley
- National Human Genome Research Institute
| | | | - Adam Gordon
- Northwestern University Feinberg School of Medicine
| | | | | | | | | | - Mullai Murugan
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | - Eric Venner
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | - Eric Boerwinkle
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | | | - Lisa Mahanta
- Laboratory for Molecular Medicine (LMM), Mass General Brigham
| | | | - Richard A Gibbs
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| | - Donna M Muzny
- Baylor College of Medicine, Human Genome Sequencing Center (HGSC)
| |
Collapse
|
7
|
Zhang Z, Chen X, Zhang W, Liu J, Xie Y, Zhang S, Stromberg AJ, Watt DS, Liu X, Wang C, Liu C. Genomic screening methodology not requiring barcoding: Single nucleotide polymorphism-based, mixed-cell screening (SMICS). Genomics 2023; 115:110666. [PMID: 37315874 PMCID: PMC10551848 DOI: 10.1016/j.ygeno.2023.110666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 05/31/2023] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Although high-throughput, cancer cell-line screening is a time-honored, important tool for anti-cancer drug development, this process involves the testing of each, individual drug in each, individual cell-line. Despite the availability of robotic liquid handling systems, this process remains a time-consuming and costly investment. The Broad Institute developed a new method called Profiling Relative Inhibition Simultaneously in Mixtures (PRISM) to screen a mixture of barcoded, tumor cell-lines. Although this methodology significantly improved the efficiency of screening large numbers of cell-lines, the barcoding process itself was tedious that requires gene transfection and subsequent selection of stable cell-lines. In this study, we developed a new, genomic approach for screening multiple cancer cell-lines using endogenous "tags" that did not require prior barcoding: single nucleotide polymorphism-based, mixed-cell screening (SMICS). The code for SMICS is available at https://github.com/MarkeyBBSRF/SMICS.
Collapse
Affiliation(s)
- Zhuwei Zhang
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY 40506, United States of America
| | - Xi Chen
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Center for Drug Innovation and Discovery, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Wen Zhang
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Jinpeng Liu
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America
| | - Yanqi Xie
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Shulin Zhang
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Arnold J Stromberg
- Department of Statistics, College of Arts and Sciences, University of Kentucky, Lexington, KY 40506, United States of America
| | - David S Watt
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America
| | - Xifu Liu
- Center for Drug Innovation and Discovery, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China.
| | - Chi Wang
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, KY 40506, United States of America.
| | - Chunming Liu
- Lucille Parker Markey Cancer Center, University of Kentucky, Lexington, KY 40536, United States of America; Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY 40536, United States of America.
| |
Collapse
|
8
|
Xu Z, Cheng S, Qiu X, Wang X, Hu Q, Shi Y, Liu Y, Lin J, Tian J, Peng Y, Jiang Y, Yang Y, Ye J, Wang Y, Meng X, Li Z, Li H, Wang Y. A pipeline for sample tagging of whole genome bisulfite sequencing data using genotypes of whole genome sequencing. BMC Genomics 2023; 24:347. [PMID: 37353738 DOI: 10.1186/s12864-023-09413-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/27/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND In large-scale high-throughput sequencing projects and biobank construction, sample tagging is essential to prevent sample mix-ups. Despite the availability of fingerprint panels for DNA data, little research has been conducted on sample tagging of whole genome bisulfite sequencing (WGBS) data. This study aims to construct a pipeline and identify applicable fingerprint panels to address this problem. RESULTS Using autosome-wide A/T polymorphic single nucleotide variants (SNVs) obtained from whole genome sequencing (WGS) and WGBS of individuals from the Third China National Stroke Registry, we designed a fingerprint panel and constructed an optimized pipeline for tagging WGBS data. This pipeline used Bis-SNP to call genotypes from the WGBS data, and optimized genotype comparison by eliminating wildtype homozygous and missing genotypes, and retaining variants with identical genomic coordinates and reference/alternative alleles. WGS-based and WGBS-based genotypes called from identical or different samples were extensively compared using hap.py. In the first batch of 94 samples, the genotype consistency rates were between 71.01%-84.23% and 51.43%-60.50% for the matched and mismatched WGS and WGBS data using the autosome-wide A/T polymorphic SNV panel. This capability to tag WGBS data was validated among the second batch of 240 samples, with genotype consistency rates ranging from 70.61%-84.65% to 49.58%-61.42% for the matched and mismatched data, respectively. We also determined that the number of genetic variants required to correctly tag WGBS data was on the order of thousands through testing six fingerprint panels with different orders for the number of variants. Additionally, we affirmed this result with two self-designed panels of 1351 and 1278 SNVs, respectively. Furthermore, this study confirmed that using the number of genetic variants with identical coordinates and ref/alt alleles, or identical genotypes could not correctly tag WGBS data. CONCLUSION This study proposed an optimized pipeline, applicable fingerprint panels, and a lower boundary for the number of fingerprint genetic variants needed for correct sample tagging of WGBS data, which are valuable for tagging WGBS data and integrating multi-omics data for biobanks.
Collapse
Affiliation(s)
- Zhe Xu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Si Cheng
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, 100069, China
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China
| | - Xin Qiu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Xiaoqi Wang
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Qiuwen Hu
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Yanfeng Shi
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yang Liu
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Jinxi Lin
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Jichao Tian
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Yongfei Peng
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Yong Jiang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Yadong Yang
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Jianwei Ye
- BioChain (Beijing) Science and Technology, Inc, Economic and Technological Development Area, 100176, Beijing, P. R. China
| | - Yilong Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Xia Meng
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Zixiao Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
| | - Hao Li
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yongjun Wang
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, 100070, China.
- Center of excellence for Omics Research (CORe), Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
- Clinical Center for Precision Medicine in Stroke, Capital Medical University, Beijing, 100069, China.
- Advanced Innovation Center for Human Brain Protection, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
9
|
Fattorini P, Previderè C, Livieri T, Zupanc T, Pajnič IZ. SNP analysis of challenging bone DNA samples using the HID-Ion AmpliSeq™ Identity Panel: facts and artefacts. Int J Legal Med 2023:10.1007/s00414-023-03019-9. [PMID: 37212920 PMCID: PMC10247551 DOI: 10.1007/s00414-023-03019-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
PCR-MPS is an emerging tool for the analysis of low-quality DNA samples. In this study, we used PCR-MPS to analyse 32 challenging bone DNA samples from three Second World War victims, which previously yielded no results in conventional STR PCR-CE typing. The Identity Panel was used with 27 cycles of PCR. Despite that we only had an average of 6.8 pg of degraded DNA as template, 30 out of 32 libraries (93.8%) produced sequencing data for about 63/90 autosomal markers per sample. Out of the 30 libraries, 14 (46.7%) yielded single source genetic profiles in agreement with the biological identity of the donor, whereas 12 cases (40.0%) resulted in SNP profiles that did not match or were mixed. The misleading outcomes for those 12 cases were likely due to hidden exogenous human contamination, as shown by the higher frequencies of allelic imbalance, unusual high frequencies of allelic drop-ins, high heterozygosity levels in the consensus profiles generated from challenging samples, and traces of amplified molecular products in four out of eight extraction negative controls. Even if the source and the time of the contamination were not identified, it is likely that it occurred along the multi-step bone processing workflow. Our results suggest that only positive identification by statistical tools (e.g. likelihood ratio) should be accepted as reliable; oppositely, the results leading to exclusion should be treated as inconclusive because of potential contamination issues. Finally, strategies are discussed for monitoring the workflow of extremely challenging bone samples in PCR-MPS experiments with an increased number of PCR cycles.
Collapse
Affiliation(s)
- Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Pavia, Italy
| | - Tommaso Livieri
- Department of Medicine, Surgery and Health, University of Trieste, Trieste, Italy
| | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia.
| |
Collapse
|
10
|
Abbassi-Daloii T, el Abdellaoui S, Voortman LM, Veeger TTJ, Cats D, Mei H, Meuffels DE, van Arkel E, 't Hoen PAC, Kan HE, Raz V. A transcriptome atlas of leg muscles from healthy human volunteers reveals molecular and cellular signatures associated with muscle location. eLife 2023; 12:80500. [PMID: 36744868 PMCID: PMC9988256 DOI: 10.7554/elife.80500] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 02/03/2023] [Indexed: 02/07/2023] Open
Abstract
Skeletal muscles support the stability and mobility of the skeleton but differ in biomechanical properties and physiological functions. The intrinsic factors that regulate muscle-specific characteristics are poorly understood. To study these, we constructed a large atlas of RNA-seq profiles from six leg muscles and two locations from one muscle, using biopsies from 20 healthy young males. We identified differential expression patterns and cellular composition across the seven tissues using three bioinformatics approaches confirmed by large-scale newly developed quantitative immune-histology procedures. With all three procedures, the muscle samples clustered into three groups congruent with their anatomical location. Concomitant with genes marking oxidative metabolism, genes marking fast- or slow-twitch myofibers differed between the three groups. The groups of muscles with higher expression of slow-twitch genes were enriched in endothelial cells and showed higher capillary content. In addition, expression profiles of Homeobox (HOX) transcription factors differed between the three groups and were confirmed by spatial RNA hybridization. We created an open-source graphical interface to explore and visualize the leg muscle atlas (https://tabbassidaloii.shinyapps.io/muscleAtlasShinyApp/). Our study reveals the molecular specialization of human leg muscles, and provides a novel resource to study muscle-specific molecular features, which could be linked with (patho)physiological processes.
Collapse
Affiliation(s)
| | - Salma el Abdellaoui
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| | - Lenard M Voortman
- Division of Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Thom TJ Veeger
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
| | - Davy Cats
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Hailiang Mei
- Sequencing Analysis Support Core, Leiden University Medical CenterLeidenNetherlands
| | - Duncan E Meuffels
- Orthopedic and Sport Medicine Department, Erasmus MC, University Medical Center RotterdamRotterdamNetherlands
| | | | - Peter AC 't Hoen
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical CenterRadboudNetherlands
| | - Hermien E Kan
- C.J. Gorter MRI Center, Department of Radiology, Leiden University Medical CenterLeidenNetherlands
- Duchenne Center NetherlandsLeidenNetherlands
| | - Vered Raz
- Department of Human Genetics, Leiden University Medical CenterLeidenNetherlands
| |
Collapse
|
11
|
Tavana N, Ting TH, Lai K, Kennerson ML, Thilakavathy K. Whole exome sequencing identifies two novel variants in PHEX and DMP1 in Malaysian children with hypophosphatemic rickets. Ital J Pediatr 2022; 48:193. [PMID: 36482408 PMCID: PMC9730657 DOI: 10.1186/s13052-022-01385-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Hypophosphatemic rickets (HR) is a genetic disease of phosphate wasting that is characterized by defective bone mineralization. The most common cause of the disease is mutations in the phosphate regulating gene with homologies to endopeptidases on the X chromosome (PHEX) gene. The aims of this study were to identify the gene variants responsible for HR in three cases of Malaysian origin from three independent families and to describe their clinical, biochemical, and radiological features. METHODS Whole exome sequencing (WES) was performed on all patients and their parents, followed by Sanger sequencing validation. Bioinformatics tools were used to provide supporting evidence for pathogenicity of variants. To confirm that a mutation is de novo, paternity test was carried out. High resolution melting curve analysis was performed to assess the allele frequency in normal controls for mutations that were found in the patients. RESULTS The patients showed typical characteristics of HR including lower limb deformity, hypophosphatemia, and elevated alkaline phosphatase. WES revealed two variants in the PHEX gene and one variant in the dentin matrix protein 1 (DMP1) gene. Two of the three variants were novel, including c.1946_1954del (p.Gly649_Arg651del) in PHEX and c.54 + 1G > A in DMP1. Our data suggests that the novel p.Gly649_Arg651del variant is likely pathogenic for HR disease. CONCLUSIONS This study extends the variant spectrum of the PHEX and DMP1 genes. Our findings indicate that WES is an advantageous approach for diagnosis of genetic diseases which are heterogeneous.
Collapse
Affiliation(s)
- Nahid Tavana
- grid.11142.370000 0001 2231 800XDepartment of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor Malaysia
| | - Tzer Hwu Ting
- grid.11142.370000 0001 2231 800XDepartment of Paediatrics, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor Malaysia
| | - Kaitao Lai
- grid.1013.30000 0004 1936 834XNorthcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW Australia ,grid.1013.30000 0004 1936 834XSydney Medical School, University of Sydney, Sydney, NSW Australia
| | - Marina L. Kennerson
- grid.1013.30000 0004 1936 834XNorthcott Neuroscience Laboratory, ANZAC Research Institute, University of Sydney, Concord, NSW Australia ,grid.414685.a0000 0004 0392 3935Molecular Medicine Laboratory, Concord Hospital, Concord, NSW Australia
| | - Karuppiah Thilakavathy
- grid.11142.370000 0001 2231 800XDepartment of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor Malaysia ,grid.11142.370000 0001 2231 800XGenetics and Regenerative Medicine Research Group, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor Malaysia
| |
Collapse
|
12
|
Samlali K, Thornbury M, Venter A. Community-led risk analysis of direct-to-consumer whole-genome sequencing. Biochem Cell Biol 2022; 100:499-509. [PMID: 35939839 DOI: 10.1139/bcb-2021-0506] [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: 12/14/2022] Open
Abstract
Direct-to-consumer (DTC) genetic testing is cheaper and more accessible than ever before; however, the intention to combine, reuse, and resell this genetic information as powerful data sets is generally hidden from the consumer. This financial gain is creating a competitive DTC market, reducing the price of whole-genome sequencing (WGS) to under 300 USD. Entering this transition from single-nucleotide polymorphism-based DTC testing to WGS DTC testing, individuals looking for access to their whole-genomic information face new privacy and security risks. Differences between WGS and other methods of consumer genetic tests are left unexplored by regulation, leading to the application of legal data anonymization methods on whole-genome data, and questionable consent methods. Large representative genomic data sets are important for research and improve the standard of medicine and personalized care. However, these data can also be used by market players, law enforcement, and governments for surveillance, population analyses, marketing purposes, and discrimination. Here, we present a summary of the state of WGS DTC genetic testing and its current regulation, through a community-based lens to expose dual-use risks in consumer-facing biotechnologies.
Collapse
Affiliation(s)
- Kenza Samlali
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Electrical and Computer Engineering, Concordia University, Montréal, QC, Canada
| | - Mackenzie Thornbury
- BricoBio Community Biology Lab, Montréal, QC, Canada.,Centre for Applied Synthetic Biology, Concordia University, Montréal, QC, Canada.,Department of Biology, Concordia University, Montréal, QC, Canada
| | - Andrei Venter
- BricoBio Community Biology Lab, Montréal, QC, Canada
| |
Collapse
|
13
|
Fierro-Monti I, Wright JC, Choudhary JS, Vizcaíno JA. Identifying individuals using proteomics: are we there yet? Front Mol Biosci 2022; 9:1062031. [PMID: 36523653 PMCID: PMC9744771 DOI: 10.3389/fmolb.2022.1062031] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/16/2022] [Indexed: 08/31/2023] Open
Abstract
Multi-omics approaches including proteomics analyses are becoming an integral component of precision medicine. As clinical proteomics studies gain momentum and their sensitivity increases, research on identifying individuals based on their proteomics data is here examined for risks and ethics-related issues. A great deal of work has already been done on this topic for DNA/RNA sequencing data, but it has yet to be widely studied in other omics fields. The current state-of-the-art for the identification of individuals based solely on proteomics data is explained. Protein sequence variation analysis approaches are covered in more detail, including the available analysis workflows and their limitations. We also outline some previous forensic and omics proteomics studies that are relevant for the identification of individuals. Following that, we discuss the risks of patient reidentification using other proteomics data types such as protein expression abundance and post-translational modification (PTM) profiles. In light of the potential identification of individuals through proteomics data, possible legal and ethical implications are becoming increasingly important in the field.
Collapse
Affiliation(s)
- Ivo Fierro-Monti
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | | | - Juan Antonio Vizcaíno
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, United Kingdom
| |
Collapse
|
14
|
Wang S, Kim M, Li W, Jiang X, Chen H, Harmanci A. Privacy-aware estimation of relatedness in admixed populations. Brief Bioinform 2022; 23:bbac473. [PMID: 36384083 PMCID: PMC10144692 DOI: 10.1093/bib/bbac473] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/07/2022] [Accepted: 10/02/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Estimation of genetic relatedness, or kinship, is used occasionally for recreational purposes and in forensic applications. While numerous methods were developed to estimate kinship, they suffer from high computational requirements and often make an untenable assumption of homogeneous population ancestry of the samples. Moreover, genetic privacy is generally overlooked in the usage of kinship estimation methods. There can be ethical concerns about finding unknown familial relationships in third-party databases. Similar ethical concerns may arise while estimating and reporting sensitive population-level statistics such as inbreeding coefficients for the concerns around marginalization and stigmatization. RESULTS Here, we present SIGFRIED, which makes use of existing reference panels with a projection-based approach that simplifies kinship estimation in the admixed populations. We use simulated and real datasets to demonstrate the accuracy and efficiency of kinship estimation. We present a secure federated kinship estimation framework and implement a secure kinship estimator using homomorphic encryption-based primitives for computing relatedness between samples in two different sites while genotype data are kept confidential. Source code and documentation for our methods can be found at https://doi.org/10.5281/zenodo.7053352. CONCLUSIONS Analysis of relatedness is fundamentally important for identifying relatives, in association studies, and for estimation of population-level estimates of inbreeding. As the awareness of individual and group genomic privacy is growing, privacy-preserving methods for the estimation of relatedness are needed. Presented methods alleviate the ethical and privacy concerns in the analysis of relatedness in admixed, historically isolated and underrepresented populations. SHORT ABSTRACT Genetic relatedness is a central quantity used for finding relatives in databases, correcting biases in genome wide association studies and for estimating population-level statistics. Methods for estimating genetic relatedness have high computational requirements, and occasionally do not consider individuals from admixed ancestries. Furthermore, the ethical concerns around using genetic data and calculating relatedness are not considered. We present a projection-based approach that can efficiently and accurately estimate kinship. We implement our method using encryption-based techniques that provide provable security guarantees to protect genetic data while kinship statistics are computed among multiple sites.
Collapse
Affiliation(s)
- Su Wang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Miran Kim
- Department of Mathematics, Hanyang University, Seoul, 04763. Republic of Korea
| | - Wentao Li
- Center for Secure Artificial intelligence For hEalthcare (SAFE), School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial intelligence For hEalthcare (SAFE), School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Han Chen
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| |
Collapse
|
15
|
Kim M, Wang S, Jiang X, Harmanci A. SVAT: Secure outsourcing of variant annotation and genotype aggregation. BMC Bioinformatics 2022; 23:409. [PMID: 36182914 PMCID: PMC9526274 DOI: 10.1186/s12859-022-04959-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 09/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background Sequencing of thousands of samples provides genetic variants with allele frequencies spanning a very large spectrum and gives invaluable insight into genetic determinants of diseases. Protecting the genetic privacy of participants is challenging as only a few rare variants can easily re-identify an individual among millions. In certain cases, there are policy barriers against sharing genetic data from indigenous populations and stigmatizing conditions. Results We present SVAT, a method for secure outsourcing of variant annotation and aggregation, which are two basic steps in variant interpretation and detection of causal variants. SVAT uses homomorphic encryption to encrypt the data at the client-side. The data always stays encrypted while it is stored, in-transit, and most importantly while it is analyzed. SVAT makes use of a vectorized data representation to convert annotation and aggregation into efficient vectorized operations in a single framework. Also, SVAT utilizes a secure re-encryption approach so that multiple disparate genotype datasets can be combined for federated aggregation and secure computation of allele frequencies on the aggregated dataset. Conclusions Overall, SVAT provides a secure, flexible, and practical framework for privacy-aware outsourcing of annotation, filtering, and aggregation of genetic variants. SVAT is publicly available for download from https://github.com/harmancilab/SVAT. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-04959-6.
Collapse
Affiliation(s)
- Miran Kim
- Department of Mathematics, Hanyang University, Seoul, 04763, Republic of Korea
| | - Su Wang
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Xiaoqian Jiang
- Center for Secure Artificial Intelligence For hEalthcare (SAFE), School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Arif Harmanci
- Center for Precision Health, School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX, 77030, USA.
| |
Collapse
|
16
|
Lan Q, Zhao C, Chen C, Xu H, Fang Y, Yao H, Zhu B. Forensic Feature Exploration and Comprehensive Genetic Insights Into Yugu Ethnic Minority and Northern Han Population via a Novel NGS-Based Marker Set. Front Genet 2022; 13:816737. [PMID: 35601485 PMCID: PMC9121381 DOI: 10.3389/fgene.2022.816737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The MPS technology has expanded the potential applications of DNA markers and increased the discrimination power of the targeted loci by taking variations in their flanking regions into consideration. Here, a collection of nuclear and extranuclear DNA markers (totally six kinds of nuclear genetic markers and mtDNA hypervariable region variations) were comprehensively and systematically assessed for polymorphism detections, further employed to dissect the population backgrounds in the Yugu ethnic group from Gansu province (Yugu) and Han population from the Inner Mongolia Autonomous Region (NMH) of China. The elevated efficiencies of the marker set in separating full sibling and challenging half sibling determination cases in parentage tests (iiSNPs), as well as predicting ancestry origins of unknown individuals from at least four continental populations (aiSNPs) and providing informative characteristic-related clues for Chinese populations (piSNPs) are highlighted in the present study. To sum up, different sets of DNA markers revealed sufficient effciencies to serve as promising tools in forensic applications. Genetic insights from the perspectives of autosomal DNA, Y chromosomal DNA, and mtDNA variations yielded that the Yugu ethnic group was genetically close related to the Han populations of the northern region. But we admit that more reference populations (like Mongolian, Tibetan, Hui, and Tu) should be incorporated to gain a refined genetic background landscape of the Yugu group in future studies.
Collapse
Affiliation(s)
- Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Congying Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chong Chen
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
| | - Hui Xu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yating Fang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, China
- Clinical Research Center of Shaanxi Province for Dental and Maxillofacial Diseases, College of Stomatology, Xi’an Jiaotong University, Xi’an, China
- *Correspondence: Bofeng Zhu,
| |
Collapse
|
17
|
Dash HR, Avila E, Jena SR, Kaitholia K, Agarwal R, Alho CS, Srivastava A, Singh AK. Forensic characterization of 124 SNPs in the central Indian population using precision ID Identity Panel through next-generation sequencing. Int J Legal Med 2021; 136:465-473. [PMID: 34748086 DOI: 10.1007/s00414-021-02742-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
With the advent of next-generation sequencing technology, SNP markers are being explored as a useful alternative to conventional capillary electrophoresis-based STR typing. Low mutation rate and short-sized amplicons are added advantages of SNP markers over the STRs. However, to achieve a sufficient level of discrimination among individuals, a higher number of SNPs need to be characterized simultaneously. Hence, the NGS technique is highly useful to analyze a sufficiently higher number of SNPs simultaneously. Though the technique is in its nascent stage, an attempt has been made to assess its usability in the central Indian population by analyzing 124 SNPs (90 autosomal and 34 Y-chromosome) in 95 individuals. Various quality parameters such as locus balance, locus strand balance, heterozygosity balance, and noise level showed a good quality sequence obtained from the Ion GeneStudio S5 instrument. Obtained frequency of SNP alleles ranged from 0.001 to 0.377 in autosomal SNPs. rs9951171 was found to be the most informative SNP in the studied population with the highest PD and lowest MP value. The cumulative MP of 90 SNPs was found to be 4.76698 × 10-37. Analysis of 34 Y-chromosome SNPs reveals 11 unique haplogroups in 54 male samples with R1a1 as the most frequent haplogroup found in 22.22% of samples. Interpopulation comparison by FST analysis, PCA plot, and STRUCTURE analysis showed genetic stratification of the studied population suggesting the utility of SNP markers present in the Precision ID Identity Panel for forensic demands of the Indian population.
Collapse
Affiliation(s)
- Hirak Ranjan Dash
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India.
| | - Eduardo Avila
- Pontifical Catholic University of Rio Grande Do Sul, Porto Alegre, Brazil
| | - Soumya Ranjan Jena
- Department of Zoology, School of Life Sciences, Ravenshaw University, Cuttack, Odisha, India
| | - Kamlesh Kaitholia
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | - Radhika Agarwal
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| | | | - Ankit Srivastava
- Institute of Forensic Science and Criminology, Bundelkhand University, Jhansi, UP, India
| | - Anil Kumar Singh
- DNA Fingerprinting Unit, Forensic Science Laboratory, Bhopal, Madhya Pradesh, India
| |
Collapse
|
18
|
Chen C, Jin X, Zhang X, Zhang W, Guo Y, Tao R, Chen A, Xu Q, Li M, Yang Y, Zhu B. Comprehensive Insights Into Forensic Features and Genetic Background of Chinese Northwest Hui Group Using Six Distinct Categories of 231 Molecular Markers. Front Genet 2021; 12:705753. [PMID: 34721519 PMCID: PMC8555763 DOI: 10.3389/fgene.2021.705753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 09/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Hui minority is predominantly composed of Chinese-speaking Islamic adherents distributed throughout China, of which the individuals are mainly concentrated in Northwest China. In the present study, we employed the length and sequence polymorphisms-based typing system of 231 molecular markers, i.e., amelogenin, 22 phenotypic-informative single nucleotide polymorphisms (PISNPs), 94 identity-informative single nucleotide polymorphisms (IISNPs), 24 Y-chromosomal short tandem repeats (Y-STRs), 56 ancestry-informative single nucleotide polymorphisms (AISNPs), 7 X-chromosomal short tandem repeats (X-STRs), and 27 autosomal short tandem repeats (A-STRs), into 90 unrelated male individuals from the Chinese Northwest Hui group to comprehensively explore its forensic characteristics and genetic background. Total of 451 length-based and 652 sequence-based distinct alleles were identified from 58 short tandem repeats (STRs) in 90 unrelated Northwest Hui individuals, denoting that the sequence-based genetic markers could pronouncedly provide more genetic information than length-based markers. The forensic characteristics and efficiencies of STRs and IISNPs were estimated, both of which externalized high polymorphisms in the Northwest Hui group and could be further utilized in forensic investigations. No significant departure from the Hardy-Weinberg equilibrium (HWE) expectation was observed after the Bonferroni correction. Additionally, four group sets of reference population data were exploited to dissect the genetic background of the Northwest Hui group separately from different perspectives, which contained 26 populations for 93 IISNPs, 58 populations for 17 Y-STRs, 26 populations for 55 AISNPs (raw data), and 109 populations for 55 AISNPs (allele frequencies). As a result, the analyses based on the Y-STRs indicated that the Northwest Hui group primarily exhibited intimate genetic relationships with reference Hui groups from Chinese different regions except for the Sichuan Hui group and secondarily displayed close genetic relationships with populations from Central and West Asia, as well as several Chinese groups. However, the AISNP analyses demonstrated that the Northwest Hui group shared more intimate relationships with current East Asian populations apart from reference Hui group, harboring the large proportion of ancestral component contributed by East Asia.
Collapse
Affiliation(s)
- Chong Chen
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xiaoye Jin
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Xingru Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Wenqing Zhang
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Yuxin Guo
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China
| | - Ruiyang Tao
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China
| | - Anqi Chen
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Department of Forensic Medicine, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiannan Xu
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Min Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,Institute of Forensic Medicine, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Yue Yang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Sciences, Ministry of Justice, Shanghai, China.,School of Basic Medicine, Inner Mongolia Medical University, Hohhot, China
| | - Bofeng Zhu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, College of Stomatology, Xi'an Jiaotong University, Xi'an, China.,Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China.,Department of Forensic Genetics, Multi-Omics Innovative Research Center of Forensic Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| |
Collapse
|
19
|
A novel computational strategy to predict the value of the evidence in the SNP-based forensic mixtures. PLoS One 2021; 16:e0247344. [PMID: 34653182 PMCID: PMC8519470 DOI: 10.1371/journal.pone.0247344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 09/30/2021] [Indexed: 11/24/2022] Open
Abstract
This study introduces a methodology for inferring the weight of the evidence (WoE) in the single nucleotide polymorphism (SNP)-typed DNA mixtures of forensic interest. First, we redefined some algebraic formulae to approach the semi-continuous calculation of likelihoods and likelihood ratios (LRs). To address the allelic dropouts, a peak height ratio index (“h,” an index of heterozygous state plausibility) was incorporated into semi-continuous formulae to act as a proxy for the “split-drop” model of calculation. Second, the original ratio at which a person of interest (POI) has entered into the mixture was inferred by evaluating the DNA amounts conferred by unique genotypes to any possible permutation of any locus of the typing protocol (unique genotypes are genotypes that appear just once in the relevant permutation). We compared this expected ratio (MRex) to all the mixing ratios emerging at all other permutations of the mixture (MRobs) using several (1 - χ2) tests to evaluate the probability of each permutation to exist in the mixture according to quantitative criteria. At the level of each permutation state, we multiplied the (1 - χ2) value to the genotype frequencies and the h index. All the products of all the permutation states were finally summed to give a likelihood value that accounts for three independent properties of the mixtures. Owing to the (1 - χ2) index and the h index, this approach qualifies as a fully continuous methodology of LR calculation. We compared the MRs and LRs emerging from our methodology to those generated by the EuroForMix software ver. 3.0.3. When the true contributors were tested as POIs, our procedure generated highly discriminant LRs that, unlike EuroForMix, never overcame the corresponding single-source LRs. When false contributors were tested as POIs, we obtained a much lower LR value than that from EuroForMix. These two findings indicate that our computational method is more reliable and realistic than EuroForMix.
Collapse
|
20
|
Walter W, Shahswar R, Stengel A, Meggendorfer M, Kern W, Haferlach T, Haferlach C. Clinical application of whole transcriptome sequencing for the classification of patients with acute lymphoblastic leukemia. BMC Cancer 2021; 21:886. [PMID: 34340673 PMCID: PMC8330044 DOI: 10.1186/s12885-021-08635-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/17/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Considering the clinical and genetic characteristics, acute lymphoblastic leukemia (ALL) is a rather heterogeneous hematological neoplasm for which current standard diagnostics require various analyses encompassing morphology, immunophenotyping, cytogenetics, and molecular analysis of gene fusions and mutations. Hence, it would be desirable to rely on a technique and an analytical workflow that allows the simultaneous analysis and identification of all the genetic alterations in a single approach. Moreover, based on the results with standard methods, a significant amount of patients have no established abnormalities and hence, cannot further be stratified. METHODS We performed WTS and WGS in 279 acute lymphoblastic leukemia (ALL) patients (B-cell: n = 211; T-cell: n = 68) to assess the accuracy of WTS, to detect relevant genetic markers, and to classify ALL patients. RESULTS DNA and RNA-based genotyping was used to ensure correct WTS-WGS pairing. Gene expression analysis reliably assigned samples to the B Cell Precursor (BCP)-ALL or the T-ALL group. Subclassification of BCP-ALL samples was done progressively, assessing first the presence of chromosomal rearrangements by the means of fusion detection. Compared to the standard methods, 97% of the recurrent risk-stratifying fusions could be identified by WTS, assigning 76 samples to their respective entities. Additionally, read-through fusions (indicative of CDKN2A and RB1 gene deletions) were recurrently detected in the cohort along with 57 putative novel fusions, with yet untouched diagnostic potentials. Next, copy number variations were inferred from WTS data to identify relevant ploidy groups, classifying an additional of 31 samples. Lastly, gene expression profiling detected a BCR-ABL1-like signature in 27% of the remaining samples. CONCLUSION As a single assay, WTS allowed a precise genetic classification for the majority of BCP-ALL patients, and is superior to conventional methods in the cases which lack entity defining genetic abnormalities.
Collapse
Affiliation(s)
- Wencke Walter
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany.
| | - Rabia Shahswar
- Department of Hematology, Hemostasis, Oncology, and Stem Cell Transplantation, Hannover Medical School, 30625, Hannover, Germany
| | - Anna Stengel
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Manja Meggendorfer
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Wolfgang Kern
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Torsten Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| | - Claudia Haferlach
- MLL Munich Leukemia Laboratory, Max-Lebsche-Platz 31, 81377, Munich, Germany
| |
Collapse
|
21
|
Karim N, Plott TJ, Durbin-Johnson BP, Rocke DM, Salemi M, Phinney BS, Goecker ZC, Pieterse MJM, Parker GJ, Rice RH. Elucidation of familial relationships using hair shaft proteomics. Forensic Sci Int Genet 2021; 54:102564. [PMID: 34315035 DOI: 10.1016/j.fsigen.2021.102564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 07/08/2021] [Accepted: 07/14/2021] [Indexed: 01/01/2023]
Abstract
This study examines the potential of hair shaft proteomic analysis to delineate genetic relatedness. Proteomic profiling and amino acid sequence analysis provide information for quantitative and statistically-based analysis of individualization and sample similarity. Protein expression levels are a function of cell-specific transcriptional and translational programs. These programs are greatly influenced by an individual's genetic background, and are therefore influenced by familial relatedness as well as ancestry and genetic disease. Proteomic profiles should therefore be more similar among related individuals than unrelated individuals. Likewise, profiles of genetically variant peptides that contain single amino acid polymorphisms, the result of non-synonymous SNP alleles, should behave similarly. The proteomically-inferred SNP alleles should also provide a basis for calculation of combined paternity and sibship indices. We test these hypotheses using matching proteomic and genetic datasets from a family of two adults and four siblings, one of which has a genetic condition that perturbs hair structure and properties. We demonstrate that related individuals, compared to those who are unrelated, have more similar proteomic profiles, profiles of genetically variant peptides and higher combined paternity indices and combined sibship indices. This study builds on previous analyses of hair shaft protein profiling and genetically variant peptide profiles in different real-world scenarios including different human hair shaft body locations and pigmentation status. It also validates the inclusion of proteomic information with other biomolecular substrates in forensic hair shaft analysis, including mitochondrial and nuclear DNA.
Collapse
Affiliation(s)
- Noreen Karim
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Tempest J Plott
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
| | - Blythe P Durbin-Johnson
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational, Science Center Biostatistics Core, University of California, Davis, USA
| | - David M Rocke
- Division of Biostatistics, Department of Public Health Sciences, Clinical and Translational, Science Center Biostatistics Core, University of California, Davis, USA
| | - Michelle Salemi
- Proteomics Core Facility, University of California, Davis, USA
| | - Brett S Phinney
- Proteomics Core Facility, University of California, Davis, USA
| | - Zachary C Goecker
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Marc J M Pieterse
- Department of Environmental Toxicology, University of California, Davis, USA
| | - Glendon J Parker
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
| | - Robert H Rice
- Department of Environmental Toxicology, University of California, Davis, USA; Forensic Science Program, University of California, Davis, USA
| |
Collapse
|
22
|
Ugrappa S, Jain A. An emergence of dental tissues in the forensic medicine for the postmortem interval estimation: A scoping review. JOURNAL OF FORENSIC SCIENCE AND MEDICINE 2021. [DOI: 10.4103/jfsm.jfsm_20_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
23
|
Hu S, Zhan W, Wang J, Xie J, Zhou W, Yang X, Zeng Y, Hu T, Duan L, Chen K, Du L, Yin A, Luo M. Establishment and application of a novel method based on single nucleotide polymorphism analysis for detecting β-globin gene cluster deletions. Sci Rep 2020; 10:18298. [PMID: 33106596 PMCID: PMC7588424 DOI: 10.1038/s41598-020-75507-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 10/12/2020] [Indexed: 12/03/2022] Open
Abstract
β-Globin gene mutations reduce or terminate the production of beta globin chains, of which approximately 10% are large deletions within the β-globin gene cluster. Because gene deletion leads to loss of heterozygosity at single nucleotide polymorphism (SNP), a novel method for detecting β-globin gene cluster deletions based on SNP heterozygosity analysis was established in this study. The location range of SNPs was selected according to the breakpoint of β-globin gene cluster deletions. SNPs were screened using bioinformatics analysis and population sequencing data. A novel method which enables genotyping of multiplex SNPs based on tetra-primer ARMS-PCR was designed and optimized. Forty clinical samples were tested in parallel by this method and MLPA to verify the performance of this method for detecting β-globin gene cluster deletion. Six informative SNPs were obtained, achieving heterozygote coverage of 93.3% in normal individuals. Genotyping of six SNPs were successfully integrated into two multiplex tetra-primer ARMS-PCR reactions. The sensitivity, specificity, positive predictive value and negative predictive value of the method for detecting β-globin gene cluster deletion were 100%, 96.30%, 92.86%, and 100%, respectively. This is a simple, cost-effective and novel method for detecting β-globin gene cluster deletions, which may be suitable for use in combination with MLPA for thalassemia molecular testing.
Collapse
Affiliation(s)
- Siqi Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetics Center, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen, Guangdong, China
| | - Wenli Zhan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jicheng Wang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Jia Xie
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Weiping Zhou
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Xiaohan Yang
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Yukun Zeng
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Tingting Hu
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Lei Duan
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China
| | - Keyi Chen
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Li Du
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Aihua Yin
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China.,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China
| | - Mingyong Luo
- Medical Genetic Centre, Guangdong Women and Children's Hospital, Guangzhou Medical University, 521-523 Xingnan Avenue, Panyu District, Guangzhou, 511400, China. .,Medical Genetic Centre, Guangdong Women and Children Hospital, Guangzhou, China.
| |
Collapse
|
24
|
Chen X, Qian W, Song Z, Li QX, Guo S. Authentication, characterization and contamination detection of cell lines, xenografts and organoids by barcode deep NGS sequencing. NAR Genom Bioinform 2020; 2:lqaa060. [PMID: 33575611 PMCID: PMC7671372 DOI: 10.1093/nargab/lqaa060] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 07/21/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
Misidentification and contamination of biobank samples (e.g. cell lines) have plagued biomedical research. Short tandem repeat (STR) and single-nucleotide polymorphism assays are widely used to authenticate biosamples and detect contamination, but with insufficient sensitivity at 5–10% and 3–5%, respectively. Here, we describe a deep NGS-based method with significantly higher sensitivity (≤1%). It can be used to authenticate human and mouse cell lines, xenografts and organoids. It can also reliably identify and quantify contamination of human cell line samples, contaminated with only small amount of other cell samples; detect and quantify species-specific components in human–mouse mixed samples (e.g. xenografts) with 0.1% sensitivity; detect mycoplasma contamination; and infer population structure and gender of human samples. By adopting DNA barcoding technology, we are able to profile 100–200 samples in a single run at per-sample cost comparable to conventional STR assays, providing a truly high-throughput and low-cost assay for building and maintaining high-quality biobanks.
Collapse
Affiliation(s)
- Xiaobo Chen
- Crown Bioscience, Inc., 218 Xinghu Road, Suzhou, Jiangsu 215400, China
| | - Wubin Qian
- Crown Bioscience, Inc., 218 Xinghu Road, Suzhou, Jiangsu 215400, China
| | - Zhenzhen Song
- Crown Bioscience, Inc., 218 Xinghu Road, Suzhou, Jiangsu 215400, China
| | - Qi-Xiang Li
- Crown Bioscience, Inc., 16550 W Bernardo Dr, Building 5, San Diego, CA 92127, USA
| | - Sheng Guo
- Crown Bioscience, Inc., 218 Xinghu Road, Suzhou, Jiangsu 215400, China
| |
Collapse
|
25
|
Fernandes M, Decouchant J, Volp M, Couto FM, Esteves-Verissimo P. DNA-SeAl: Sensitivity Levels to Optimize the Performance of Privacy-Preserving DNA Alignment. IEEE J Biomed Health Inform 2020; 24:907-915. [DOI: 10.1109/jbhi.2019.2914952] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
26
|
Kumar H, Panigrahi M, Chhotaray S, Parida S, Chauhan A, Bhushan B, Gaur GK, Mishra BP, Singh RK. Comparative analysis of five different methods to design a breed-specific SNP panel for cattle. Anim Biotechnol 2019; 32:130-136. [PMID: 31364913 DOI: 10.1080/10495398.2019.1646266] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Single nucleotide polymorphisms (SNPs) have now replaced microsatellite markers in several species for various genetic investigations like parentage assignment, genetic breed composition, assessment for individuality and, most popularly, as a useful tool in genomic selection. However, such a resource, which can offer to assist breed identification in a cost-effective manner is still not explored in cattle breeding programs. In our study, we have tried to describe methods for reducing the number of SNPs to develop a breed-specific panel. We have used SNP data from Dryad open public access repository. Starting from a global dataset of 178 animals belonging to 10 different breeds, we selected five panels each comprising of similar number of SNPs using different methods i.e., Delta, Pairwise Wright's FST, informativeness for assignment, frequent item feature selection (FIFS) and minor allele frequency-linkage disequilibrium (MAF-LD) based method. MAF-LD based method has been recently developed by us for construction of breed-specific SNP panels. The STRUCTURE software analysis of MAF-LD based method showed appropriate clustering in comparison to other panels. Later, the panel of 591 breed-specific SNPs was called to their respective breeds using Venny 2.1.0 and UGent web tools software. Breed-specific SNPs were later annotated by using various Bioinformatics softwares.
Collapse
Affiliation(s)
- Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Supriya Chhotaray
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Anuj Chauhan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - G K Gaur
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - B P Mishra
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| | - R K Singh
- Division of Animal Biotechnology, ICAR-Indian Veterinary Research Institute, Bareilly, India
| |
Collapse
|
27
|
Pfeifer JD. Identity determination in diagnostic surgical pathology. Semin Diagn Pathol 2019; 36:355-365. [PMID: 31196743 DOI: 10.1053/j.semdp.2019.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
From a technical perspective, specimen identity determination in surgical pathology over the last several decades has primarily focused on analysis of repetitive DNA sequences, specifically microsatellite repeats. However, a number of techniques have recently been developed that have similar, if not greater, utility in surgical pathology, most notably analysis of single nucleotide polymorphism (SNPs) and gene panels by next generation sequencing (NGS). For cases with an extremely limited sample or a degraded sample, sequence analysis of mitochondrial DNA continues to be the method of choice. From a diagnostic perspective, interest in identity determination in surgical pathology is usually centered on resolving issues of specimen provenance due to specimen labeling/accessioning deficiencies and possible contamination, but is also frequently performed in cases for which the patient's clinical course following definitive therapy is remarkably atypical, in cases of an unexpected diagnosis, and by patient request for "peace of mind". However, the methods used for identity determination have a much broader range of applications in surgical pathology beyond tissue provenance analysis. The methods can be used to provide ancillary information for cases in which the histomorphology is not definitively diagnostic, as for example for tumors that have a virtually identical microscopic appearance but for which the differential diagnosis includes synchronous/metachronous tumors versus a metastasis, and for the diagnosis of hydropic early gestations versus hydatidiform molar pregnancies. The methods also have utility in several other clinical settings, for example to rule out a donor-transmitted malignancy in a transplant recipient, to monitor bone marrow transplant engraftment, and to evaluate natural chimerism.
Collapse
Affiliation(s)
- John D Pfeifer
- Department of Pathology, Washington University School of Medicine, Campus Box 8118, 660 S. Euclid Ave, St. Louis, MO 63110, USA.
| |
Collapse
|
28
|
Lo E, Bonizzoni M, Hemming-Schroeder E, Ford A, Janies DA, James AA, Afrane Y, Etemesi H, Zhou G, Githeko A, Yan G. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
|
29
|
Amorim A, Pinto N. Big data in forensic genetics. Forensic Sci Int Genet 2018; 37:102-105. [PMID: 30142461 DOI: 10.1016/j.fsigen.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 07/23/2018] [Accepted: 08/01/2018] [Indexed: 12/16/2022]
Abstract
The potential and difficulties of the application of genome wide data in forensics are analyzed. We argue that, besides statistical, computational, ethical, economic and technical validation problems, the state of the art of population genetics theory is insufficient to deal with the forensic use of this type of data. In order to keep the current standards of quantifying and reporting genetic evidence, namely in kinship analyses and identification, substantial improvement in the theoretical framework should be reached, since to obtain genome-wide results is to provide the experts with data that they cannot quantify the corresponding evidentiary value. Therefore, while a satisfactory, generalized theoretical and biostatistical modelling is not achieved, it may well be wiser to improve the already established approaches to a limited, pre-defined number of validated genetic markers, amenable to a consensual handling and reporting. Whole genome population analyses will prove extremely useful in selecting the best suited and most efficient of those markers.
Collapse
Affiliation(s)
- António Amorim
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Nadia Pinto
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto, Portugal; Instituto de Investigação e Inovação em Saúde (i3s), Universidade do Porto, Porto, Portugal; CMUP, Centro de Matemática da Universidade do Porto, Porto, Portugal.
| |
Collapse
|