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Wang Y, Cui Y, Zhou X, Han J. Development of a high-throughput resequencing array for the detection of pathogenic mutations in osteogenesis imperfecta. PLoS One 2015; 10:e0119553. [PMID: 25742658 PMCID: PMC4350936 DOI: 10.1371/journal.pone.0119553] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Accepted: 01/30/2015] [Indexed: 01/29/2023] Open
Abstract
Objective Osteogenesis imperfecta (OI) is a rare inherited skeletal disease, characterized by bone fragility and low bone density. The mutations in this disorder have been widely reported to be on various exonal hotspots of the candidate genes, including COL1A1, COL1A2, CRTAP, LEPRE1, and FKBP10, thus creating a great demand for precise genetic tests. However, large genome sizes make the process daunting and the analyses, inefficient and expensive. Therefore, we aimed at developing a fast, accurate, efficient, and cheaper sequencing platform for OI diagnosis; and to this end, use of an advanced array-based technique was proposed. Method A CustomSeq Affymetrix Resequencing Array was established for high-throughput sequencing of five genes simultaneously. Genomic DNA extraction from 13 OI patients and 85 normal controls and amplification using long-range PCR (LR-PCR) were followed by DNA fragmentation and chip hybridization, according to standard Affymetrix protocols. Hybridization signals were determined using GeneChip Sequence Analysis Software (GSEQ). To examine the feasibility, the outcome from new resequencing approach was validated by conventional capillary sequencing method. Result Overall call rates using resequencing array was 96–98% and the agreement between microarray and capillary sequencing was 99.99%. 11 out of 13 OI patients with pathogenic mutations were successfully detected by the chip analysis without adjustment, and one mutation could also be identified using manual visual inspection. Conclusion A high-throughput resequencing array was developed that detects the disease-associated mutations in OI, providing a potential tool to facilitate large-scale genetic screening for OI patients. Through this method, a novel mutation was also found.
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Affiliation(s)
- Yao Wang
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- Shandong Institute of Endocrine and Metabolic Diseases, Shandong Academy of Medical Sciences, Ji’nan, Shandong, China
| | - Yazhou Cui
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Xiaoyan Zhou
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
| | - Jinxiang Han
- Shandong Academy of Medical Sciences, Shandong Medical Biotechnological Center, Key Laboratory for Biotech Drugs of the Ministry of Health, Ji’nan, Shandong, China
- * E-mail:
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Tran B, Dancey JE, Kamel-Reid S, McPherson JD, Bedard PL, Brown AM, Zhang T, Shaw P, Onetto N, Stein L, Hudson TJ, Neel BG, Siu LL. Cancer Genomics: Technology, Discovery, and Translation. J Clin Oncol 2012; 30:647-60. [DOI: 10.1200/jco.2011.39.2316] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In recent years, the increasing awareness that somatic mutations and other genetic aberrations drive human malignancies has led us within reach of personalized cancer medicine (PCM). The implementation of PCM is based on the following premises: genetic aberrations exist in human malignancies; a subset of these aberrations drive oncogenesis and tumor biology; these aberrations are actionable (defined as having the potential to affect management recommendations based on diagnostic, prognostic, and/or predictive implications); and there are highly specific anticancer agents available that effectively modulate these targets. This article highlights the technology underlying cancer genomics and examines the early results of genome sequencing and the challenges met in the discovery of new genetic aberrations. Finally, drawing from experiences gained in a feasibility study of somatic mutation genotyping and targeted exome sequencing led by Princess Margaret Hospital–University Health Network and the Ontario Institute for Cancer Research, the processes, challenges, and issues involved in the translation of cancer genomics to the clinic are discussed.
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Affiliation(s)
- Ben Tran
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Janet E. Dancey
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Suzanne Kamel-Reid
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - John D. McPherson
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Philippe L. Bedard
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Andrew M.K. Brown
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Tong Zhang
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Patricia Shaw
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Nicole Onetto
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Lincoln Stein
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Thomas J. Hudson
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Benjamin G. Neel
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
| | - Lillian L. Siu
- Ben Tran, Philippe L. Bedard, and Lillian L. Siu, Princess Margaret Hospital, University Health Network, University of Toronto; Janet E. Dancey, John D. McPherson, Andrew M.K. Brown, Nicole Onetto, Lincoln Stein, and Thomas J. Hudson, Ontario Institute for Cancer Research; Suzanne Kamel-Reid, Tong Zhang, and Patricia Shaw, Toronto General Hospital, University Health Network, University of Toronto; John D. McPherson, Nicole Onetto, Lincoln Stein, Thomas J. Hudson, and Benjamin G. Neel, University of
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Pandya GA, McEllistrem MC, Venepally P, Holmes MH, Jarrahi B, Sanka R, Liu J, Karamycheva SA, Bai Y, Fleischmann RD, Peterson SN. Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains. PLoS One 2011; 6:e15950. [PMID: 21264340 PMCID: PMC3018475 DOI: 10.1371/journal.pone.0015950] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Accepted: 12/01/2010] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND While the pneumococcal protein conjugate vaccines reduce the incidence in invasive pneumococcal disease (IPD), serotype replacement remains a major concern. Thus, serotype-independent protection with vaccines targeting virulence genes, such as PspA, have been pursued. PspA is comprised of diverse clades that arose through recombination. Therefore, multi-locus sequence typing (MLST)-defined clones could conceivably include strains from multiple PspA clades. As a result, a method is needed which can both monitor the long-term epidemiology of the pneumococcus among a large number of isolates, and analyze vaccine-candidate genes, such as pspA, for mutations and recombination events that could result in 'vaccine escape' strains. METHODOLOGY We developed a resequencing array consisting of five conserved and six variable genes to characterize 72 pneumococcal strains. The phylogenetic analysis of the 11 concatenated genes was performed with the MrBayes program, the single nucleotide polymorphism (SNP) analysis with the DNA Sequence Polymorphism program (DnaSP), and the recombination event analysis with the recombination detection package (RDP). RESULTS The phylogenetic analysis correlated with MLST, and identified clonal strains with unique PspA clades. The DnaSP analysis correlated with the serotype-specific diversity detected using MLST. Serotypes associated with more than one ST complex had a larger degree of sequence polymorphism than a serotype associated with one ST complex. The RDP analysis confirmed the high frequency of recombination events in the pspA gene. CONCLUSIONS The phylogenetic tree correlated with MLST, and detected multiple PspA clades among clonal strains. The genetic diversity of the strains and the frequency of recombination events in the mosaic gene, pspA were accurately assessed using the DnaSP and RDP programs, respectively. These data provide proof-of-concept that resequencing arrays could play an important role within research and clinical laboratories in both monitoring the molecular epidemiology of the pneumococcus and detecting 'vaccine escape' strains among vaccine-candidate genes.
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Affiliation(s)
- Gagan A. Pandya
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - M. Catherine McEllistrem
- Veterans Affairs Pittsburgh Healthcare System, Pittsburgh, Pennsylvania, United States of America
| | - Pratap Venepally
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael H. Holmes
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Behnam Jarrahi
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Ravi Sanka
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Jia Liu
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Svetlana A. Karamycheva
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Yun Bai
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Robert D. Fleischmann
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Scott N. Peterson
- Pathogen Functional Genomics Resource Center, J. Craig Venter Institute, Rockville, Maryland, United States of America
- * E-mail:
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