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Chin H, Benton MC, Yang L, Poon KS, Tan KML, Jamuar SS, Foo R, Law HY, Goh DL, Chong SS, de Sessions PF. Clinical application of targeted long read sequencing in prenatal beta-thalassemia testing and genetic counseling. Mol Genet Genomic Med 2024; 12:e2285. [PMID: 37740604 PMCID: PMC10767580 DOI: 10.1002/mgg3.2285] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/24/2023] Open
Abstract
BACKGROUND Beta thalassemia, related to HBB mutation and associated with elevated hemoglobin A2 (HbA2), is an important genetic hemoglobinopathy with high incidences of disease and carrier rates in Singapore. Carrier screening is essential to facilitate prenatal counseling and testing. However, when individuals with elevated HbA2 do not have an identifiable HBB disease-associated variant, there is ambiguity on risk to their offspring. METHODS We describe a case report of a proband with elevated HbA2, no identifiable HBB disease-associated variant, whose partner was a beta thalassemia carrier. Through clinical HBB gene sequencing, multiplex ligation-dependent probe amplification (MLPA) analysis, as well as targeted Nanopore long read sequencing of selected genes, we performed a complete analysis of HBB including the promoter region, 5'UTR and coding gene sequence, as well as evaluation for potential modifier variants and other rare structural variants. RESULTS This process identified that the proband was heterozygous for KLF1:c.544T>C (p.Phe182Leu), a potential functional polymorphism previously known to be associated with benign elevated HbA2 levels. The presence of disease variants in the HBB locus was excluded. CONCLUSION This finding provided clarity and enabled family planning for the proband and her family.
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Affiliation(s)
- Hui‐Lin Chin
- Division of Genetics and Metabolism, Department of PaediatricsKhoo Teck Puat‐National University Children's Medical Institute, National University HospitalSingaporeSingapore
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | | | - Lin Yang
- Oxford Nanopore TechnologiesSingaporeSingapore
| | - Kok Siong Poon
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
| | - Karen M. L. Tan
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
| | - Saumya S. Jamuar
- Genetics Service, Department of PaediatricsKK Women's and Children's HospitalSingaporeSingapore
| | - Roger Foo
- Cardiovascular Research Institute, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Hai Yang Law
- DNA Diagnostic and Research LaboratoryKK Women's and Children's HospitalSingaporeSingapore
| | - Denise Li‐Meng Goh
- Division of Genetics and Metabolism, Department of PaediatricsKhoo Teck Puat‐National University Children's Medical Institute, National University HospitalSingaporeSingapore
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Samuel S. Chong
- Department of Paediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of Laboratory MedicineNational University HospitalSingaporeSingapore
- Department of Obstetrics and GynaecologyYong Loo Lin School of Medicine, National University of SingaporeSingaporeSingapore
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Nguyen MT, Nguyen TT, Nguyen DB, Nguyen TM, Nguyen KN, Ngo VNM, Nguyen VD, Tran NA, Lian M, Tan ASC, Chong SS, Dang TT. Robust preimplantation genetic testing of the common F8 Inv22 pathogenic variant of severe hemophilia A using a highly polymorphic multi-marker panel encompassing the paracentric inversion. Thromb J 2023; 21:108. [PMID: 37864173 PMCID: PMC10588207 DOI: 10.1186/s12959-023-00552-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/09/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Hemophilia A (HEMA) is an X-linked bleeding disorder caused by reduced/absent coagulation factor VIII expression, as a result of pathogenic variants in the F8 gene. Preimplantation prevention of HEMA should ideally include direct pathogenic F8 variant detection, complemented by linkage analysis of flanking markers to identify the high-risk F8 allele. Linkage analysis is particularly indispensable when the pathogenic variant cannot be detected directly or identified. This study evaluated the suitability of a panel of F8 intragenic and extragenic short tandem repeat markers for standalone linkage-based preimplantation genetic testing for monogenic disorder (PGT-M) of the Inv22 pathogenic variant, an almost 600 kb paracentric inversion responsible for almost half of all severe HEMA globally, for which direct detection is challenging. METHODS Thirteen markers spanning 1 Mb and encompassing both F8 and the Inv22 inversion interval were genotyped in 153 unrelated females of Viet Kinh ethnicity. RESULTS All individuals were heterozygous for ≥ 1 marker, ~ 90% were heterozygous for ≥ 1 of the five F8 intragenic markers, and almost 98% were heterozygous for ≥ 1 upstream (telomeric) and ≥ 1 downstream (centromeric) markers. A prospective PGT-M couple at risk of transmitting F8 Inv22 were fully informative at four marker loci (2 intra-inversion, 1 centromeric, 1 telomeric) and partially informative at another five (2 intra-inversion, 3 centromeric), allowing robust phasing of low- and high-risk haplotypes. In vitro fertilization produced three embryos, all of which clearly inherited the low-risk maternal allele, enabling reliable unaffected diagnoses. A single embryo transfer produced a clinical pregnancy, which was confirmed as unaffected by amniocentesis and long-range PCR, and a healthy baby girl was delivered at term. CONCLUSION Robust and reliable PGT-M of HEMA, including the common F8 Inv22 pathogenic variant, can be achieved with sufficient informative intragenic and flanking markers.
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Affiliation(s)
- Minh Tam Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thanh Tung Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Duy Bac Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Thi Mai Nguyen
- National Institute of Hematology and Blood Transfusion, Hanoi, Vietnam
| | - Kim Ngan Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Van Nhat Minh Ngo
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Van Dieu Nguyen
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Ngoc Anh Tran
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Centre, National University Centre for Women and Children, National University Hospital, Singapore, Singapore
| | - Arnold S C Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore
| | - Samuel S Chong
- Preimplantation Genetic Diagnosis Centre, National University Centre for Women and Children, National University Hospital, Singapore, Singapore.
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
| | - Tien Truong Dang
- Department of Anatomy, Vietnam Military Medical University, Hanoi, Vietnam.
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Yap JYY, Goh LSH, Lim AJW, Chong SS, Lim LJ, Lee CG. Machine Learning Identifies a Signature of Nine Exosomal RNAs That Predicts Hepatocellular Carcinoma. Cancers (Basel) 2023; 15:3749. [PMID: 37509410 PMCID: PMC10377993 DOI: 10.3390/cancers15143749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 07/30/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related death worldwide. Although alpha fetoprotein (AFP) remains a commonly used serological marker of HCC, the sensitivity and specificity of AFP in detecting HCC is often limited. Exosomal RNA has emerged as a promising diagnostic tool for various cancers, but its use in HCC detection has yet to be fully explored. Here, we employed Machine Learning on 114,602 exosomal RNAs to identify a signature that can predict HCC. The exosomal expression data of 118 HCC patients and 112 healthy individuals were stratified split into Training, Validation and Unseen Test datasets. Feature selection was then performed on the initial training dataset using permutation importance, and the predictive performance of the selected features were tested on the validation dataset using Support Vector Machine (SVM) Classifier. A minimum of nine features were identified to be predictive of HCC and these nine features were then evaluated across six different models in an unseen test set. These features, mainly in the immune, platelet/neutrophil and cytoskeletal pathways, exhibited good predictive performance with ROC-AUC from 0.79-0.88 in the unseen test set. Hence, these nine exosomal RNAs have potential to be clinically useful minimally invasive biomarkers for HCC.
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Affiliation(s)
- Josephine Yu Yan Yap
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- NUS Graduate School, National University of Singapore, Singapore 119077, Singapore
| | - Laura Shih Hui Goh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Ashley Jun Wei Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Samuel S Chong
- Department of Paediatrics and Obstetrics & Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119074, Singapore
| | - Lee Jin Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117596, Singapore
- NUS Graduate School, National University of Singapore, Singapore 119077, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore 168583, Singapore
- Duke-NUS Medical School, Singapore 169857, Singapore
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4
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Tan VJ, Liu T, Arifin Z, Pak B, Tan ASC, Wong S, Khor CC, Yang H, Lee CG, Huang Z, Choolani MA, Chong SS. Third-Generation Single-Molecule Sequencing for Preimplantation Genetic Testing of Aneuploidy and Segmental Imbalances. Clin Chem 2023:hvad062. [PMID: 37477572 DOI: 10.1093/clinchem/hvad062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 03/22/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND Current strategies for preimplantation genetic testing for aneuploidy or structural rearrangements (PGT-A/SR) rely mainly on next-generation sequencing (NGS) and microarray platforms, which are robust but require expensive instrumentation. We explored the suitability of third-generation single-molecule sequencing as a PGT-A/SR screening platform for both aneuploidy and segmental imbalance. METHODS Single-cell and multicell replicates from aneuploid or segmentally unbalanced cell lines (n = 208) were SurePlex-amplified, randomized, and subjected to (a) Nanopore-based single-molecule sequencing (Oxford Nanopore Technologies) and (b) NGS using a leading commercial PGT-A solution (Illumina VeriSeq PGS). Archival SurePlex-amplified trophectoderm biopsy samples (n = 96) previously analyzed using the commercial kit were blinded and reanalyzed using Nanopore. RESULTS Nanopore-based PGT-A identified the specific aberration in 95.45% (84/88) and 97.78% (88/90) of single-/multicells with an aneuploidy or segmental imbalance (10-30.5 Mb), respectively. Comparison against the commercial kit's results revealed concordances of 98.86% (87/88) and 98.89% (89/90) for the aneuploid and segmentally unbalanced (10-30.5 Mb aberration) samples, respectively. Detection sensitivity for smaller segmental imbalances (5-5.8 Mb aberration, n = 30) decreased markedly on both platforms. Nanopore-based PGT-A reanalysis of trophectoderm biopsy samples was 97.92% (94/96) concordant with the commercial kit results. CONCLUSION Up to 24 SurePlex-amplified single-cell, multicell, or trophectoderm samples could be sequenced in a single MinION flow-cell for subsequent preimplantation genetic testing for aneuploidy or structural rearrangements (PGT-A/SR) analysis, with results obtainable in ≤3 days and at per-sample costs that are competitive with commercial offerings. Nanopore's third-generation single-molecule sequencing represents a viable alternative to current commercial NGS-based PGT-A solutions for aneuploidy and segmental imbalance (≥10 Mb) screening of single-/multicell or trophectoderm biopsy samples.
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Affiliation(s)
- Vivienne J Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Timing Liu
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zainul Arifin
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Beatrice Pak
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Arnold S C Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Simin Wong
- Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore
| | - Chiea-Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Zhongwei Huang
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Mahesh A Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Preimplantation Genetic Diagnosis Centre, Department of Obstetrics and Gynaecology, National University Hospital, Singapore
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore
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Lian M, Zhao M, Phang GP, Rajan-Babu IS, Chong SS. Triplet-primed PCR and Melting Curve Analysis for Rapid Molecular Screening of Spinocerebellar Ataxia Types 1, 2, and 3. Bio Protoc 2023; 13:e4704. [PMID: 37397792 PMCID: PMC10308190 DOI: 10.21769/bioprotoc.4704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/27/2023] [Accepted: 04/14/2023] [Indexed: 07/04/2023] Open
Abstract
There are more than 40 types of spinocerebellar ataxia (SCA), most of which are caused by abnormal expansion of short tandem repeats at various gene loci. These phenotypically similar disorders require molecular testing at multiple loci by fluorescent PCR and capillary electrophoresis to identify the causative repeat expansion. We describe a simple strategy to screen for the more common SCA1, SCA2, and SCA3 by rapidly detecting the abnormal CAG repeat expansion at the ATXN1, ATXN2, and ATXN3 loci using melting curve analysis of triplet-primed PCR products. Each of the three separate assays employs a plasmid DNA carrying a known repeat size to generate a threshold melt peak temperature, which effectively distinguishes expansion-positive samples from those without a repeat expansion. Samples that are screened positive based on their melt peak profiles are subjected to capillary electrophoresis for repeat sizing and genotype confirmation. These screening assays are robust and provide accurate detection of the repeat expansion while eliminating the need for fluorescent PCR and capillary electrophoresis for every sample.
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Affiliation(s)
- Mulias Lian
- Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Indhu-Shree Rajan-Babu
- Department of Medical Genetics, University of British Columbia, and Children’s & Women’s Hospital, Vancouver, British Columbia, Canada
| | - Samuel S. Chong
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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6
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Dolzhenko E, Weisburd B, Ibañez K, Rajan-Babu IS, Anyansi C, Bennett MF, Billingsley K, Carroll A, Clamons S, Danzi MC, Deshpande V, Ding J, Fazal S, Halman A, Jadhav B, Qiu Y, Richmond PA, Saunders CT, Scheffler K, van Vugt JJFA, Zwamborn RRAJ, Chong SS, Friedman JM, Tucci A, Rehm HL, Eberle MA. REViewer: haplotype-resolved visualization of read alignments in and around tandem repeats. Genome Med 2022; 14:84. [PMID: 35948990 PMCID: PMC9367089 DOI: 10.1186/s13073-022-01085-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/11/2022] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Expansions of short tandem repeats are the cause of many neurogenetic disorders including familial amyotrophic lateral sclerosis, Huntington disease, and many others. Multiple methods have been recently developed that can identify repeat expansions in whole genome or exome sequencing data. Despite the widely recognized need for visual assessment of variant calls in clinical settings, current computational tools lack the ability to produce such visualizations for repeat expansions. Expanded repeats are difficult to visualize because they correspond to large insertions relative to the reference genome and involve many misaligning and ambiguously aligning reads. RESULTS We implemented REViewer, a computational method for visualization of sequencing data in genomic regions containing long repeat expansions and FlipBook, a companion image viewer designed for manual curation of large collections of REViewer images. To generate a read pileup, REViewer reconstructs local haplotype sequences and distributes reads to these haplotypes in a way that is most consistent with the fragment lengths and evenness of read coverage. To create appropriate training materials for onboarding new users, we performed a concordance study involving 12 scientists involved in short tandem repeat research. We used the results of this study to create a user guide that describes the basic principles of using REViewer as well as a guide to the typical features of read pileups that correspond to low confidence repeat genotype calls. Additionally, we demonstrated that REViewer can be used to annotate clinically relevant repeat interruptions by comparing visual assessment results of 44 FMR1 repeat alleles with the results of triplet repeat primed PCR. For 38 of these alleles, the results of visual assessment were consistent with triplet repeat primed PCR. CONCLUSIONS Read pileup plots generated by REViewer offer an intuitive way to visualize sequencing data in regions containing long repeat expansions. Laboratories can use REViewer and FlipBook to assess the quality of repeat genotype calls as well as to visually detect interruptions or other imperfections in the repeat sequence and the surrounding flanking regions. REViewer and FlipBook are available under open-source licenses at https://github.com/illumina/REViewer and https://github.com/broadinstitute/flipbook respectively.
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Affiliation(s)
- Egor Dolzhenko
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Ben Weisburd
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Kristina Ibañez
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Indhu-Shree Rajan-Babu
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada ,grid.13097.3c0000 0001 2322 6764Department of Medical and Molecular Genetics, King’s College London, Strand, London, WC2R 2LS UK
| | - Christine Anyansi
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Mark F. Bennett
- grid.1042.70000 0004 0432 4889Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, University of Melbourne, Parkville, VIC 3052 Australia ,grid.410678.c0000 0000 9374 3516Epilepsy Research Centre, Department of Medicine, University of Melbourne, Austin Health, Heidelberg, VIC 3084 Australia
| | - Kimberley Billingsley
- grid.419475.a0000 0000 9372 4913Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD USA ,grid.419475.a0000 0000 9372 4913Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD USA
| | - Ashley Carroll
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Samuel Clamons
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Matt C. Danzi
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Viraj Deshpande
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Jinhui Ding
- grid.419475.a0000 0000 9372 4913Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892 USA
| | - Sarah Fazal
- grid.26790.3a0000 0004 1936 8606Dr. John T. Macdonald Foundation Department of Human Genetics and John P. Hussman Institute for Human Genomics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Andreas Halman
- grid.1055.10000000403978434Peter MacCallum Cancer Centre, Melbourne, VIC 3000 Australia ,grid.1008.90000 0001 2179 088XSir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Bharati Jadhav
- grid.59734.3c0000 0001 0670 2351Department of Genetics and Genomic Sciences and Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Yunjiang Qiu
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Phillip A. Richmond
- grid.414137.40000 0001 0684 7788BC Children’s Hospital Research Institute, Vancouver, BC V5Z 4H4 Canada
| | | | - Konrad Scheffler
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
| | - Joke J. F. A. van Vugt
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Ramona R. A. J. Zwamborn
- grid.5477.10000000120346234Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Samuel S. Chong
- grid.4280.e0000 0001 2180 6431Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.4280.e0000 0001 2180 6431Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228 Singapore ,grid.412106.00000 0004 0621 9599Department of Laboratory Medicine, National University Hospital, Singapore, 119074 Singapore
| | - Jan M. Friedman
- grid.17091.3e0000 0001 2288 9830Department of Medical Genetics, University of British Columbia and Children’s & Women’s Hospital, Vancouver, BC V6H3N1 Canada
| | - Arianna Tucci
- grid.4868.20000 0001 2171 1133William Harvey Research Institute, Queen Mary University of London, London, EC1M 6BQ UK
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Michael A. Eberle
- grid.185669.50000 0004 0507 3954Illumina Inc., San Diego, CA 92122 USA
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Rajan-Babu IS, Lian M, Chong SS. Triplet-Primed PCR Assays for Accurate Screening of FMR1 CGG Repeat Expansion and Genotype Verification. Curr Protoc 2022; 2:e427. [PMID: 35609145 DOI: 10.1002/cpz1.427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Fragile X syndrome and other fragile X-associated disorders are caused by the full-mutation (>200 copies) and premutation (55 to 200 copies) expansion, respectively, of the CGG short tandem repeat in the fragile X messenger ribonucleoprotein 1 (FMR1) gene. Clinical diagnostic laboratories use Southern blot analysis and polymerase chain reaction (PCR)-based tests to detect and/or size the FMR1 CGG repeats. The development of sensitive and high-throughput triplet-primed PCR (TP-PCR) assays has diminished the need to subject all samples to Southern blot analysis, which is both labor- and time-intensive. In this article, we describe two direct TP-PCR (dTP-PCR) assays for the detection of FMR1 CGG repeat expansions. We outline a protocol that is based on melting curve analysis of dTP-PCR amplicons for a rapid and cost-effective first-tier screening and identification of individuals with premutation and full-mutation expansions. We also describe a protocol that employs capillary electrophoresis to resolve the dTP-PCR amplicon fragments and to estimate the repeat sizes of normal (5 to 44 copies), intermediate (45 to 54 copies), and premutation alleles, as well as to detect full mutations and determine the structure of the FMR1 alleles. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for melting curve analysis Basic Protocol 2: Melting curve analysis of direct triplet-primed PCR amplicons on the Rotor-Gene Q MD × 5plex high-resolution melt platform Alternate Protocol: Melting curve analysis of direct triplet-primed PCR amplicons on the LightCycler 480 system Basic Protocol 3: Generation of direct triplet-primed PCR melting curve analysis profiles Basic Protocol 4: Direct triplet-primed PCR master mix preparation and amplification of the FMR1 CGG repeat locus for capillary electrophoresis Basic Protocol 5: Generation of control FMR1 plasmids for direct triplet-primed PCR melting curve analysis Basic Protocol 6: Sanger sequencing assay to verify FMR1 CGG repeat size and structure of plasmid DNA controls.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.,Children's & Women's Hospital, Vancouver, British Columbia, Canada
| | - Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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8
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Rajan-Babu IS, Phang GP, Law HY, Lee CG, Chong SS. High-Throughput Methylation-Specific Triplet-Primed PCR and Melting Curve Analysis for Selective and Reliable Identification of Actionable FMR1 Genotypes. J Mol Diagn 2022; 24:241-252. [PMID: 35038595 DOI: 10.1016/j.jmoldx.2021.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/26/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
Methylated FMR1 full-mutation expansions cause fragile X syndrome. FMR1 premutation carriers are susceptible to other late-onset conditions, and women with premutation are at risk of transmitting a fully expanded FMR1 allele to offspring. Identification of individuals with actionable FMR1 genotypes (full-mutation males and females, and premutation females at risk for primary ovarian insufficiency and/or having fragile X-affected offspring) can enable timely access to intervention services and genetic counseling. This study presents a rapid, first-tier test based on melting curve analysis of methylation-specific triplet-primed PCR amplicons (msTP-PCR MCA) for concurrent detection of FMR1 CGG-repeat expansions and their methylation status. The msTP-PCR MCA assay was optimized on 20 fragile X reference samples, and its performance was evaluated on 111 peripheral blood-derived DNA samples from patients who have undergone prior molecular testing with PCR and/or Southern blot analysis. The msTP-PCR MCA assay detected all samples with a methylated FMR1 CGG-repeat expansion, and had sensitivity, specificity, positive predictive value, and negative predictive values of 100%, 92.06%, 91.1%, and 100%, respectively. The msTP-PCR MCA assay identified premutation/full-mutation mosaicism down to 1%, detected skewed inactivation in females with FMR1 expansions, and enabled selective identification of all individuals with an actionable FMR1 genotype. The msTP-PCR MCA assay may aid in fragile X screening of at-risk populations and newborns and voluntary carrier screening of women of reproductive age.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Medical Genetics, University of British Columbia, and Children's and Women's Hospital, Vancouver, British Columbia, Canada.
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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9
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Lim AJW, Lim LJ, Ooi BNS, Koh ET, Tan JWL, Chong SS, Khor CC, Tucker-Kellogg L, Leong KP, Lee CG. Functional coding haplotypes and machine-learning feature elimination identifies predictors of Methotrexate Response in Rheumatoid Arthritis patients. EBioMedicine 2022; 75:103800. [PMID: 35022146 PMCID: PMC8808170 DOI: 10.1016/j.ebiom.2021.103800] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Major challenges in large scale genetic association studies include not only the identification of causative single nucleotide polymorphisms (SNPs), but also accounting for SNP-SNP interactions. This study thus proposes a novel feature engineering approach integrating potentially functional coding haplotypes (pfcHap) with machine-learning (ML) feature selection to identify biologically meaningful, possibly causative genetic factors, that take into consideration potential SNP-SNP interactions within the pfcHap, to best predict for methotrexate (MTX) response in rheumatoid arthritis (RA) patients. METHODS Exome sequencing from 349 RA patients were analysed, of which they were split into training and unseen test set. Inferred pfcHaps were combined with 30 non-genetic features to undergo ML recursive feature elimination with cross-validation using the training set. Predictive capacity and robustness of the selected features were assessed using six popular machine learning models through a train set cross-validation and evaluated in an unseen test set. FINDINGS Significantly, 100 features (95 pfcHaps, 5 non-genetic factors) were identified to have good predictive performance (AUC: 0.776-0.828; Sensitivity: 0.656-0.813; Specificity: 0.684-0.868) across all six ML models in an unseen test dataset for the prediction of MTX response in RA patients. INTERPRETATION Majority of the predictive pfcHap SNPs were predicted to be potentially functional and some of the genes in which the pfcHap resides in were identified to be associated with previously reported MTX/RA pathways. FUNDING Singapore Ministry of Health's National Medical Research Council (NMRC) [NMRC/CBRG/0095/2015; CG12Aug17; CGAug16M012; NMRC/CG/017/2013]; National Cancer Center Research Fund and block funding Duke-NUS Medical School.; Singapore Ministry of Education Academic Research Fund Tier 2 grant MOE2019-T2-1-138.
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Affiliation(s)
- Ashley J W Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lee Jin Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Brandon N S Ooi
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Ee Tzun Koh
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
| | - Justina Wei Lynn Tan
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore
| | - Samuel S Chong
- Dept of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chiea Chuen Khor
- Division of Human Genetics, Genome Institute of Singapore, Singapore
| | - Lisa Tucker-Kellogg
- Centre for Computational Biology, and Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore
| | - Khai Pang Leong
- Department of Rheumatology, Allergy and Immunology, Tan Tock Seng Hospital, Singapore; Clinical Research & Innovation Office, Tan Tock Seng Hospital, Singapore.
| | - Caroline G Lee
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Div of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore; Duke-NUS Medical School, Singapore; NUS Graduate School, National University of Singapore, Singapore.
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10
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Poon KS, Su LL, Chong SS, Tan KML. A Novel Indel in the Alpha Globin 2 (HBA2) Gene Resulting in False Positive -α3.7 on Multiplex gap-PCR Assay. Clin Chem 2021; 67:1284-1287. [PMID: 34333591 DOI: 10.1093/clinchem/hvab113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/03/2021] [Indexed: 11/14/2022]
Affiliation(s)
- Kok-Siong Poon
- Department of Laboratory Medicine, National University Hospital, Singapore
| | - Lin Lin Su
- Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynaecology, National University Hospital, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Samuel S Chong
- Department of Laboratory Medicine, National University Hospital, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Preimplantation Genetic Diagnosis Centre, Khoo Teck Puat-National University Children's Medical Institute, National University Hospital, Singapore
| | - Karen Mei-Ling Tan
- Department of Laboratory Medicine, National University Hospital, Singapore
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11
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Han J, Thurnherr T, Chung AYF, Goh BKP, Chow PKH, Chan CY, Cheow PC, Lee SY, Lim TKH, Chong SS, Ooi LLPJ, Lee CG. Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. Cancers (Basel) 2021; 13:cancers13112772. [PMID: 34199580 PMCID: PMC8199648 DOI: 10.3390/cancers13112772] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/21/2021] [Accepted: 05/24/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary Here, we present a novel strategy to identify key signatures of clinically-relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate the prognosis of HCC patients, by integrating clinicopathological features, circRNA and mRNA expression profiles. Five master circRNAs were identified and experimentally demonstrated to upregulate proliferate and promote transformation. Through further integration with miRNA-expression profiles, clinically-relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. The most up-regulated nodal-circRNA, circGPC3 was experimentally demonstrated to up-regulate cell-cycle, migration and invasion. circGPC3 was found to act as a sponge of miR-378a-3p to regulate ASPM expression and modulate cell transformation. These 5 nodal circRNAs has potential to be good prognostic biomarkers with good prognostic performance. circGPC3 has great potential to be a promising non-invasive prognostic biomarker for early HCC. We have thus demonstrated the robustness of bioinformatically-predicted master circRNAs in clinically-relevant, circRNA-mRNA networks, underscoring the important roles that these identified deregulated key/master circRNAs play in HCC. Abstract Hepatocellular carcinoma (HCC) is one of the most common and lethal cancers worldwide. Here, we present a novel strategy to identify key circRNA signatures of clinically relevant co-expressed circRNA-mRNA networks in pertinent cancer-pathways that modulate prognosis of HCC patients, by integrating clinic-pathological features, circRNA and mRNA expression profiles. Through further integration with miRNA expression profiles, clinically relevant competing-endogenous-RNA (ceRNA) networks of circRNA-miRNA-mRNAs were constructed. At least five clinically relevant nodal-circRNAs, co-expressed with numerous genes, were identified from the circRNA-mRNA networks. These nodal circRNAs upregulated proliferation (except circRaly) and transformation in cells. The most upregulated nodal-circRNA, circGPC3, associated with higher-grade tumors and co-expressed with 33 genes, competes with 11 mRNAs for two shared miRNAs. circGPC3 was experimentally demonstrated to upregulate cell-cycle and migration/invasion in both transformed and non-transformed liver cell-lines. circGPC3 was further shown to act as a sponge of miR-378a-3p to regulate APSM (Abnormal spindle-like microcephaly associated) expression and modulate cell transformation. This study identifies 5 key nodal master circRNAs in a clinically relevant circRNA-centric network that are significantly associated with poorer prognosis of HCC patients and promotes tumorigenesis in cell-lines. The identification and characterization of these key circRNAs in clinically relevant circRNA-mRNA and ceRNA networks may facilitate the design of novel strategies targeting these important regulators for better HCC prognosis.
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Affiliation(s)
- Jian Han
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - Thomas Thurnherr
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
| | - Alexander Y. F. Chung
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Brian K. P. Goh
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Pierce K. H. Chow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Chung Yip Chan
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Peng Chung Cheow
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Ser Yee Lee
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
| | - Tony K. H. Lim
- Department of Pathology, Singapore General Hospital, Singapore 169608, Singapore;
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
| | - London L. P. J. Ooi
- Department of Hepato-Pancreato-Biliary & Transplant Surgery, Singapore General Hospital, Singapore 169608, Singapore; (A.Y.F.C.); (B.K.P.G.); (P.K.H.C.); (C.Y.C.); (P.C.C.); (S.Y.L.); (L.L.P.J.O.)
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Department of Surgical Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore;
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore;
- Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School Singapore, Singapore 169547, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore 169610, Singapore
- Correspondence: ; Tel.: +65-65163251
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12
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Nagarathinam I, Chong SS, B. K. T, Justin Margret J, Venkataraman V, Natarajan Padmavathy K, Srisailapathy CRS. FMR1 gene CGG repeat distribution among the three individual cohorts with intellectual disability, autism, and primary ovarian insufficiency from Tamil Nadu, Southern India. Adv Genet (Hoboken) 2021; 2:e10048. [PMID: 36618123 PMCID: PMC9744524 DOI: 10.1002/ggn2.10048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Fragile X syndrome is the most common genetic cause of intellectual disability (ID) and is also well known to have a role in primary ovarian insufficiency (POI) and fragile X-associated tremor ataxia syndrome (FXTAS) that expresses across generations. The objective was to compare the CGG repeat variants in FMR1 gene among three correlating cohorts of ID, autism and idiopathic POI. Thirty-six patients with ID, 12 with autism spectrum disorder (ASD) and 13 females with idiopathic POI were screened for FMR1 CGG repeat size by fluorescent methylation-specific PCR and GeneScan analysis, irrespective of Hagerman checklist clinical scores. Among 29 males and seven females, 11 FMR1 allelic variants ranging from 21 to >200 CGG repeats were observed. Three (CF2-3, 39-5, 44-2) out of 29 males had full mutation alleles accounting for a 10.34% incidence of FXS among idiopathic ID males. One of them was a mosaic for CGG repeats with both premutation and full mutation alleles. The frequency of fragile X syndrome is high among patients with idiopathic ID; they also had a high score for the clinical check list. A cascade testing that begins with checklist evaluation prior to DNA analysis will be cost-effective for establishing early diagnosis in South India. With the huge disease burden, there is a need for the establishment of more molecular diagnostics and self-help groups for fragile X syndrome.
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Affiliation(s)
- Indhumathi Nagarathinam
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical SciencesUniversity of MadrasChennaiIndia,Department of Medical Genetics, Laboratory Services, Apollo Main HospitalChennaiIndia
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore,Department of Obstetrics and Gynaecology, Yong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Thelma B. K.
- Department of GeneticsUniversity of DelhiNew DelhiIndia
| | - Jeffrey Justin Margret
- Department of Genetics, Dr. ALM Post Graduate Institute of Basic Medical SciencesUniversity of MadrasChennaiIndia
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13
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Ooi BNS, Raechell, Ying AF, Koh YZ, Jin Y, Yee SWL, Lee JHS, Chong SS, Tan JWC, Liu J, Lee CG, Drum CL. Robust Performance of Potentially Functional SNPs in Machine Learning Models for the Prediction of Atorvastatin-Induced Myalgia. Front Pharmacol 2021; 12:605764. [PMID: 33967749 PMCID: PMC8100589 DOI: 10.3389/fphar.2021.605764] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
Statins can cause muscle symptoms resulting in poor adherence to therapy and increased cardiovascular risk. We hypothesize that combinations of potentially functional SNPs (pfSNPs), rather than individual SNPs, better predict myalgia in patients on atorvastatin. This study assesses the value of potentially functional single nucleotide polymorphisms (pfSNPs) and employs six machine learning algorithms to identify the combination of SNPs that best predict myalgia. Methods: Whole genome sequencing of 183 Chinese, Malay and Indian patients from Singapore was conducted to identify genetic variants associated with atorvastatin induced myalgia. To adjust for confounding factors, demographic and clinical characteristics were also examined for their association with myalgia. The top factor, sex, was then used as a covariate in the whole genome association analyses. Variants that were highly associated with myalgia from this and previous studies were extracted, assessed for potential functionality (pfSNPs) and incorporated into six machine learning models. Predictive performance of a combination of different models and inputs were compared using the average cross validation area under ROC curve (AUC). The minimum combination of SNPs to achieve maximum sensitivity and specificity as determined by AUC, that predict atorvastatin-induced myalgia in most, if not all the six machine learning models was determined. Results: Through whole genome association analyses using sex as a covariate, a larger proportion of pfSNPs compared to non-pf SNPs were found to be highly associated with myalgia. Although none of the individual SNPs achieved genome wide significance in univariate analyses, machine learning models identified a combination of 15 SNPs that predict myalgia with good predictive performance (AUC >0.9). SNPs within genes identified in this study significantly outperformed SNPs within genes previously reported to be associated with myalgia. pfSNPs were found to be more robust in predicting myalgia, outperforming non-pf SNPs in the majority of machine learning models tested. Conclusion: Combinations of pfSNPs that were consistently identified by different machine learning models to have high predictive performance have good potential to be clinically useful for predicting atorvastatin-induced myalgia once validated against an independent cohort of patients.
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Affiliation(s)
- Brandon N S Ooi
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Raechell
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | | | - Yong Zher Koh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore
| | - Yu Jin
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Sherman W L Yee
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore
| | | | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Jack W C Tan
- Department of Cardiology, National Heart Centre Singapore, Singapore, Singapore
| | - Jianjun Liu
- Genome Institute of Singapore, Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Dundee, Singapore.,Duke-NUS Graduate School, Singapore, Singapore.,Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
| | - Chester L Drum
- Department of Medicine, Yong Loo Lin School of Medicine, Cardiovascular Research Institute, National University of Singapore, Singapore, Singapore.,Translational Laboratory in Genetic Medicine, Singapore, Singapore
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14
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Lim LJ, Ling LH, Neo YP, Chung AY, Goh BK, Chow PK, Chan CY, Cheow PC, Lee SY, Lim TK, Chong SS, Ooi LLPJ, Lee CG. Highly deregulated lncRNA LOC is associated with overall worse prognosis in Hepatocellular Carcinoma patients. J Cancer 2021; 12:3098-3113. [PMID: 33976720 PMCID: PMC8100808 DOI: 10.7150/jca.56340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/16/2021] [Indexed: 12/24/2022] Open
Abstract
Although numerous long non-coding RNAs (lncRNAs) were reported to be deregulated in Hepatocellular Carcinoma (HCC), experimentally characterized, and/or associated with patient's clinical characteristics, there is, thus far, minimal concerted research strategy to identify deregulated lncRNAs that modulate prognosis of HCC patients. Here, we present a novel strategy where we identify lncRNAs, which are not only de-regulated in HCC patients, but are also associated with pertinent clinical characteristics, potentially contributing to the prognosis of HCC patients. LOC101926913 (LOC) was further characterized because it is the most highly differentially expressed amongst those that are associated with the most number of clinical features (tumor-stage, vascular and tumor invasion and poorer overall survival). Experimental gain- and loss-of-function manipulation of LOC in liver cell-lines highlight LOC as a potential onco-lncRNA promoting cell proliferation, anchorage independent growth and invasion. LOC expression in cells up-regulated genes involved in GTPase-activities and downregulated genes associated with cellular detoxification, oxygen- and drug-transport. Hence, LOC may represent a novel therapeutic target, modulating prognosis of HCC patients through up-regulating GTPase-activities and down-regulating detoxification, oxygen- and drug-transport. This strategy may thus be useful for the identification of clinically relevant lncRNAs as potential biomarkers/targets that modulate prognosis in other cancers as well.
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Affiliation(s)
- Lee Jin Lim
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Lay Hiang Ling
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yu Pei Neo
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-NUS Medical School, Singapore
| | - Alexander Y.F. Chung
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Brian K.P. Goh
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Pierce K.H. Chow
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
- Dept of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Chung Yip Chan
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Peng Chung Cheow
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Ser Yee Lee
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
| | - Tony K.H. Lim
- Dept of Pathology, Singapore General Hospital, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - London L. P. J. Ooi
- Dept of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore
- Duke-NUS Medical School, Singapore
- Dept of Surgical Oncology, National Cancer Centre Singapore, Singapore
| | - Caroline G. Lee
- Dept of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Duke-NUS Medical School, Singapore
- Div of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
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15
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Lian M, Zhao M, Phang GP, Soong YT, Yoon CS, Lee CG, Law HY, Chong SS. Rapid Molecular Screen of Spinocerebellar Ataxia Types 1, 2, and 3 by Triplet-Primed PCR and Melting Curve Analysis. J Mol Diagn 2021; 23:565-576. [PMID: 33618058 DOI: 10.1016/j.jmoldx.2021.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 12/02/2020] [Accepted: 01/12/2021] [Indexed: 11/16/2022] Open
Abstract
The autosomal dominantly inherited spinocerebellar ataxias (SCAs) can be caused by dynamic mutations of short tandem repeats within various genes. Because of the significant clinical overlap among the various SCA types, molecular screening of multiple genetic loci by fluorescent PCR and capillary electrophoresis is necessary to identify the causative repeat expansion. We describe a simple, rapid, and inexpensive strategy to screen for CAG repeat expansion mutations at the ATXN1, ATXN2, and ATXN3 loci using melting curve analysis of triplet-primed PCR products. Plasmid DNAs of known repeat sizes were used to generate threshold melt peak temperatures, which rapidly and effectively distinguish samples carrying an expanded allele from those carrying nonexpanded alleles. Melting curve analysis-positive samples were confirmed by capillary electrophoresis sizing of the triplet-primed PCR products. All three assays achieved 100% sensitivity, with 95% CIs of 67.86% to 100% (SCA1), 74.65% to 100% (SCA2), and 91.58% to 100% (SCA3). The SCA1 assay also achieved 100% specificity (95% CI, 97.52%-100%), whereas the SCA2 and SCA3 assays achieved specificity of 99.46% (95% CI, 96.56%-99.97%) and 99.32% (95% CI, 95.70%-99.96%), respectively. These screening assays provide robust and highly accurate detection of expanded alleles and are amenable to large-scale screening while minimizing the need for capillary electrophoresis sizing for every sample.
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Affiliation(s)
- Mulias Lian
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore
| | - Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Gui-Ping Phang
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Yun-Ting Soong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Chui-Sheun Yoon
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore; Division of Medical Sciences, National Cancer Center Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore; Pediatrics Academic Clinical Program, Duke-NUS Graduate Medical School, Singapore
| | - Samuel S Chong
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore; Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Department of Laboratory Medicine, National University Hospital, Singapore.
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16
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Zhao M, Cheah FSH, Tan ASC, Lian M, Phang GP, Agarwal A, Chong SS. Robust Preimplantation Genetic Testing of Huntington Disease by Combined Triplet-Primed PCR Analysis of the HTT CAG Repeat and Multi-Microsatellite Haplotyping. Sci Rep 2019; 9:16481. [PMID: 31712634 PMCID: PMC6848083 DOI: 10.1038/s41598-019-52769-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/23/2019] [Indexed: 12/13/2022] Open
Abstract
Huntington disease (HD) is a lethal neurodegenerative disorder caused by expansion of a CAG repeat within the huntingtin (HTT) gene. Disease prevention can be facilitated by preimplantation genetic testing for this monogenic disorder (PGT-M). We developed a strategy for HD PGT-M, involving whole genome amplification (WGA) followed by combined triplet-primed PCR (TP-PCR) for HTT CAG repeat expansion detection and multi-microsatellite marker genotyping for disease haplotype phasing. The strategy was validated and tested pre-clinically in a simulated PGT-M case before clinical application in five cycles of a PGT-M case. The assay reliably and correctly diagnosed all embryos, even where allele dropout (ADO) occurred at the HTT CAG repeat locus or at one or more linked markers. Ten of the 27 embryos analyzed were diagnosed as unaffected. Four embryo transfers were performed, two of which involved fresh cycle double embryo transfers and two were frozen-thawed single embryo transfers. Pregnancies were achieved from each of the frozen-thawed single embryo transfers and confirmed to be unaffected by amniocentesis, culminating in live births at term. This strategy enhances diagnostic confidence for PGT-M of HD and can also be employed in situations where disease haplotype phase cannot be established prior to the start of PGT-M.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Felicia Siew Hong Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Arnold Sia Chye Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Gui Ping Phang
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Anupriya Agarwal
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore. .,Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
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17
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Zhao M, Lian M, Cheah FSH, Tan ASC, Agarwal A, Chong SS. Identification of Novel Microsatellite Markers Flanking the SMN1 and SMN2 Duplicated Region and Inclusion Into a Single-Tube Tridecaplex Panel for Haplotype-Based Preimplantation Genetic Testing of Spinal Muscular Atrophy. Front Genet 2019; 10:1105. [PMID: 31781167 PMCID: PMC6851269 DOI: 10.3389/fgene.2019.01105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/11/2019] [Indexed: 12/12/2022] Open
Abstract
Preimplantation genetic testing for the monogenic disorder (PGT-M) spinal muscular atrophy (SMA) is significantly improved by supplementation of SMN1 deletion detection with marker-based linkage analysis. To expand the availability of informative markers for PGT-M of SMA, we identified novel non-duplicated and highly polymorphic microsatellite markers closely flanking the SMN1 and SMN2 duplicated region. Six of the novel markers within 0.5 Mb of the 1.7 Mb duplicated region containing SMN1 and SMN2 (SMA6863, SMA6873, SMA6877, SMA7093, SMA7115, and SMA7120) and seven established markers (D5S1417, D5S1413, D5S1370, D5S1408, D5S610, D5S1999, and D5S637), all with predicted high heterozygosity values, were selected and optimized in a tridecaplex PCR panel, and their polymorphism indices were determined in two populations. Observed marker heterozygosities in the Chinese and Caucasian populations ranged from 0.54 to 0.86, and 98.4% of genotyped individuals (185 of 188) were heterozygous for ≥2 markers on either side of SMN1. The marker panel was evaluated for disease haplotype phasing using single cells from two parent–child trios after whole-genome amplification, and applied to a clinical IVF (in vitro fertilization) PGT-M cycle in an at-risk couple, in parallel with SMN1 deletion detection. Both direct and indirect test methods determined that none of five tested embryos were at risk for SMA, with haplotype analysis further identifying one embryo as unaffected and four as carriers. Fresh transfer of the unaffected embryo did not lead to implantation, but subsequent frozen-thaw transfer of a carrier embryo produced a pregnancy, with fetal genotype confirmed by amniocentesis, and a live birth at term.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mulias Lian
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Felicia S H Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Arnold S C Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Anupriya Agarwal
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology, National University Hospital, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
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18
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Bachtiar M, Jin Y, Wang J, Tan TW, Chong SS, Ban KHK, Lee CGL. Architecture of population-differentiated polymorphisms in the human genome. PLoS One 2019; 14:e0224089. [PMID: 31622447 PMCID: PMC6797171 DOI: 10.1371/journal.pone.0224089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 10/04/2019] [Indexed: 12/25/2022] Open
Abstract
Population variation in disease and other phenotype are partly attributed to single nucleotide polymorphisms (SNPs) in the human genome. Due to selection pressure, two individuals from the same ancestral population have more genetic similarity compared to individuals from further geographic regions. Here, we elucidated the genomic population differentiation pattern, by interrogating >22,000,000 SNPs. Majority of population-differentiated (pd) SNPs (~95%), including the potentially functional (pf) (~84%) subset reside in non-genic regions, compared to the proportion of all SNPs (58%) found in non-genic regions. This suggests that differences between populations are more likely due to differences in gene regulation rather than protein function. Actin Cytoskeleton, Axonal Guidance and Protein Kinase A signaling pathways are enriched with genes carrying at least three pdSNPs (enriched pdGenes), while Antigen Presentation, Hepatic Fibrosis and Huntington Disease Signalling pathways are over-represented by enriched pf-pdGenes. An inverse correlation between chromosome size and the proportion of pd-/pf-pdSNPs was observed. Smaller chromosomes have relatively more of such SNPs including genes carrying these SNPs. Genes associated with common diseases and enriched with these pd-/pfpdSNPs are localized to 11 different chromosomes, with immune-related disease pd/pf-pdGenes mainly residing in chromosome 6 while neurological disease pd/pf-pdGenes residing in smaller chromosomes including chromosome 21/22. The associated diseases were reported to show population differences in incidence, severity and/or etiology. In summary, this study highlights the non-sporadic nature of population differentiation footprint in the human genome, which can potentially lead to the identification of genomic regions that play roles in the manifestation of phenotypic differences, including in disease predisposition and drug response.
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Affiliation(s)
- Maulana Bachtiar
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore
| | - Yu Jin
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore
| | - Jingbo Wang
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Tin Wee Tan
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- National Supercomputing Centre Singapore, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Kenneth H. K. Ban
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Caroline G. L. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Cellular & Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore
- Cancer & Stem Cell Biology Programme, Duke-NUS Graduate Medical School, Singapore
- * E-mail:
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19
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Jin Y, Lee WY, Toh ST, Tennakoon C, Toh HC, Chow PKH, Chung AYF, Chong SS, Ooi LLPJ, Sung WK, Lee CGL. Comprehensive analysis of transcriptome profiles in hepatocellular carcinoma. J Transl Med 2019; 17:273. [PMID: 31429776 PMCID: PMC6701074 DOI: 10.1186/s12967-019-2025-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/14/2019] [Indexed: 12/31/2022] Open
Abstract
Background Hepatocellular carcinoma is the second most deadly cancer with late presentation and limited treatment options, highlighting an urgent need to better understand HCC to facilitate the identification of early-stage biomarkers and uncover therapeutic targets for the development of novel therapies for HCC. Methods Deep transcriptome sequencing of tumor and paired non-tumor liver tissues was performed to comprehensively evaluate the profiles of both the host and HBV transcripts in HCC patients. Differential gene expression patterns and the dys-regulated genes associated with clinical outcomes were analyzed. Somatic mutations were identified from the sequencing data and the deleterious mutations were predicted. Lastly, human-HBV chimeric transcripts were identified, and their distribution, potential function and expression association were analyzed. Results Expression profiling identified the significantly upregulated TP73 as a nodal molecule modulating expression of apoptotic genes. Approximately 2.5% of dysregulated genes significantly correlated with HCC clinical characteristics. Of the 110 identified genes, those involved in post-translational modification, cell division and/or transcriptional regulation were upregulated, while those involved in redox reactions were downregulated in tumors of patients with poor prognosis. Mutation signature analysis identified that somatic mutations in HCC tumors were mainly non-synonymous, frequently affecting genes in the micro-environment and cancer pathways. Recurrent mutations occur mainly in ribosomal genes. The most frequently mutated genes were generally associated with a poorer clinical prognosis. Lastly, transcriptome sequencing suggest that HBV replication in the tumors of HCC patients is rare. HBV-human fusion transcripts are a common observation, with favored HBV and host insertion sites being the HBx C-terminus and gene introns (in tumors) and introns/intergenic-regions (in non-tumors), respectively. HBV-fused genes in tumors were mainly involved in RNA binding while those in non-tumors tissues varied widely. These observations suggest that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts may occur during tumorigenesis. Conclusions Transcriptome sequencing of HCC patients reveals key cancer molecules and clinically relevant pathways deregulated/mutated in HCC patients and suggests that while HBV may integrate randomly during chronic infection, selective expression of functional chimeric transcripts likely occur during the process of tumorigenesis.
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Affiliation(s)
- Yu Jin
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Wai Yeow Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | - Soo Ting Toh
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore
| | | | - Han Chong Toh
- Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Pierce Kah-Hoe Chow
- Duke-NUS Medical School, Singapore, 169547, Singapore.,Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore
| | - Alexander Y-F Chung
- Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119228, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, 119074, Singapore
| | - London L-P-J Ooi
- Department of Surgery, Singapore General Hospital, Singapore, 169608, Singapore.,Department of Surgical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
| | - Wing-Kin Sung
- Genome Institute of Singapore, Singapore, Singapore.,School of Computing, National University of Singapore, Singapore, Singapore
| | - Caroline G-L Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119077, Singapore. .,Division of Medical Sciences, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Level 6, Lab 5, 11 Hospital Drive, Singapore, 169610, Singapore. .,Duke-NUS Medical School, Singapore, 169547, Singapore.
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20
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Rajan-Babu IS, Chong SS. Triplet-Repeat Primed PCR and Capillary Electrophoresis for Characterizing the Fragile X Mental Retardation 1 CGG Repeat Hyperexpansions. Methods Mol Biol 2019; 1972:199-210. [PMID: 30847793 DOI: 10.1007/978-1-4939-9213-3_14] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Fragile X mental retardation 1 (FMR1) CGG repeat expansions cause fragile X syndrome-the leading monogenic form of intellectual disability-and increase the risk for fragile X-associated tremor ataxia syndrome and fragile X-associated primary ovarian insufficiency. Southern blot (SB) analysis is the current gold standard test for FMR1 molecular diagnosis. Several polymerase chain reaction (PCR)-based methods are now available for sizing FMR1 CGG repeat expansions. These methods offer higher diagnostic sensitivity and specificity compared to SB analysis, significantly reduce the turnaround time and increase throughput. In this chapter, we describe a triplet-repeat primed PCR protocol that employs capillary electrophoresis to resolve the derived amplicon products, enabling precise determination of the FMR1 genotypes in both males and females and characterization of the CGG repeat structure.
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Affiliation(s)
- Indhu-Shree Rajan-Babu
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Medical Genetics, The University of British Columbia, Vancouver, BC, Canada
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore, Singapore. .,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore.
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21
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Lim LJ, Wong SYS, Huang F, Lim S, Chong SS, Ooi LL, Kon OL, Lee CG. Roles and Regulation of Long Noncoding RNAs in Hepatocellular Carcinoma. Cancer Res 2019; 79:5131-5139. [PMID: 31337653 DOI: 10.1158/0008-5472.can-19-0255] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/06/2019] [Accepted: 07/19/2019] [Indexed: 01/21/2023]
Abstract
Next-generation sequencing has uncovered thousands of long noncoding RNAs (lncRNA). Many are reported to be aberrantly expressed in various cancers, including hepatocellular carcinoma (HCC), and play key roles in tumorigenesis. This review provides an in-depth discussion of the oncogenic mechanisms reported to be associated with deregulated HCC-associated lncRNAs. Transcriptional expression of lncRNAs in HCC is modulated through transcription factors, or epigenetically by aberrant histone acetylation or DNA methylation, and posttranscriptionally by lncRNA transcript stability modulated by miRNAs and RNA-binding proteins. Seventy-four deregulated lncRNAs have been identified in HCC, of which, 52 are upregulated. This review maps the oncogenic roles of these deregulated lncRNAs by integrating diverse datasets including clinicopathologic features, affected cancer phenotypes, associated miRNA and/or protein-interacting partners as well as modulated gene/protein expression. Notably, 63 deregulated lncRNAs are significantly associated with clinicopathologic features of HCC. Twenty-three deregulated lncRNAs associated with both tumor and metastatic clinical features were also tumorigenic and prometastatic in experimental models of HCC, and eight of these mapped to known cancer pathways. Fifty-two upregulated lncRNAs exhibit oncogenic properties and are associated with prominent hallmarks of cancer, whereas 22 downregulated lncRNAs have tumor-suppressive properties. Aberrantly expressed lncRNAs in HCC exert pleiotropic effects on miRNAs, mRNAs, and proteins. They affect multiple cancer phenotypes by altering miRNA and mRNA expression and stability, as well as through effects on protein expression, degradation, structure, or interactions with transcriptional regulators. Hence, these insights reveal novel lncRNAs as potential biomarkers and may enable the design of precision therapy for HCC.
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Affiliation(s)
- Lee Jin Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Samuel Y S Wong
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Feiyang Huang
- NUS High School of Math and Science, Singapore, Singapore
| | - Sheng Lim
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.,Raffles Institution, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - London Lucien Ooi
- Duke-NUS Graduate Medical School, Singapore, Singapore.,Department of Hepato-Pancreato-Biliary and Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Oi Lian Kon
- Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore. .,Division of Cellular and Molecular Research, Humphrey Oei Institute of Cancer Research, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore, Singapore
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22
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Jin Y, Wong YS, Goh BKP, Chan CY, Cheow PC, Chow PKH, Lim TKH, Goh GBB, Krishnamoorthy TL, Kumar R, Ng TP, Chong SS, Tan HH, Chung AYF, Ooi LLPJ, Chang JPE, Tan CK, Lee CGL. Circulating microRNAs as Potential Diagnostic and Prognostic Biomarkers in Hepatocellular Carcinoma. Sci Rep 2019; 9:10464. [PMID: 31320713 PMCID: PMC6639394 DOI: 10.1038/s41598-019-46872-8] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/18/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is the fifth most common cancer with high mortality, due to late diagnosis and limited treatment options. Blood miRNAs, which circulate in a highly stable, cell-free form, show promise as novel potential biomarkers for early detection of HCC. Whole miRNome profiling was performed to identify deregulated miRNAs between HCC and normal healthy (NH) volunteers. These deregulated miRNAs were validated in an independent cohort of HCC, NH and chronic Hepatitis B (CHB) volunteers and finally in a 3rd cohort comprising NH, CHB, cirrhotic and HCC volunteers to evaluate miRNA changes during disease progression. The associations between circulating miRNAs and liver-damage markers, clinicopathological characteristics and survival outcomes were analysed to identify prognostic markers. Twelve miRNAs are differentially expressed between HCC and NH individuals in all three cohorts. Five upregulated miRNAs (miR-122-5p, miR-125b-5p, miR-885-5p, miR-100-5p and miR-148a-3p) in CHB, cirrhosis and HCC patients are potential biomarkers for CHB infection, while miR-34a-5p can be a biomarker for cirrhosis. Notably, four miRNAs (miR-1972, miR-193a-5p, miR-214-3p and miR-365a-3p) can distinguish HCC from other non-HCC individuals. Six miRNAs are potential prognostic markers for overall survival.
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Affiliation(s)
- Yu Jin
- Division of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Ye Shen Wong
- Division of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore, Singapore
| | - Brian K P Goh
- Department of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Chung Yip Chan
- Department of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Peng Chung Cheow
- Department of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - Pierce K H Chow
- Division of Surgical Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Tony K H Lim
- Department of Pathology, Singapore General Hospital, Singapore, Singapore
| | - George B B Goh
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore
| | | | - Rajneesh Kumar
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Tze Pin Ng
- Department of Psychological Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Hwee Huang Tan
- Blood Services Group, Health Sciences Authority, Singapore, Singapore
| | - Alexander Y F Chung
- Department of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore
| | - London Lucien P J Ooi
- Department of Hepato-pancreato-biliary & Transplant Surgery, Singapore General Hospital, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Jason P E Chang
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore
| | - Chee Kiat Tan
- Department of Gastroenterology & Hepatology, Singapore General Hospital, Singapore, Singapore.
| | - Caroline G L Lee
- Division of Cellular & Molecular Research, National Cancer Centre Singapore, Singapore, Singapore. .,Duke-NUS Graduate Medical School, Singapore, Singapore. .,Department of Biochemistry, National University of Singapore, Singapore, Singapore.
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23
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Lian M, Lee CG, Chong SS. Robust Preimplantation Genetic Testing Strategy for Myotonic Dystrophy Type 1 by Bidirectional Triplet-Primed Polymerase Chain Reaction Combined With Multi-microsatellite Haplotyping Following Whole-Genome Amplification. Front Genet 2019; 10:589. [PMID: 31316546 PMCID: PMC6611416 DOI: 10.3389/fgene.2019.00589] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 06/04/2019] [Indexed: 12/25/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is caused by expansion of the DMPK CTG trinucleotide repeat. Disease transmission to offspring can be avoided through prenatal diagnosis or preimplantation genetic testing for monogenic disorders (PGT-M). We describe a robust strategy for DM1 PGT-M that can be applied to virtually any at-risk couple. This strategy utilizes whole-genome amplification, followed by triplet-primed PCR (TP-PCR) detection of expanded DMPK alleles, in parallel with single-tube haplotype analysis of 12 closely linked and highly polymorphic microsatellite markers. Bidirectional TP-PCR and dodecaplex marker PCR assays were optimized and validated on whole-genome amplified single lymphoblasts isolated from DM1 reference cell lines, and tested on a simulated PGT-M case comprising a parent-offspring trio and three simulated embryos. Bidirectional DMPK TP-PCR reliably detects repeat expansions even in the presence of non-CTG interruptions at either end of the expanded allele. Misdiagnoses, diagnostic ambiguity, and couple-specific assay customization are further minimized by the use of multi-marker haplotyping, preventing the loss of potentially unaffected embryos for transfer.
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Affiliation(s)
- Mulias Lian
- Department of Pediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore, Singapore.,Division of Medical Sciences, National Cancer Center, Singapore, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
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24
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Leferink M, Wong DPW, Cai S, Yeo M, Ho J, Lian M, Kamsteeg EJ, Chong SS, Haer-Wigman L, Guan M. Robust and accurate detection and sizing of repeats within the DMPK gene using a novel TP-PCR test. Sci Rep 2019; 9:8280. [PMID: 31164682 PMCID: PMC6547747 DOI: 10.1038/s41598-019-44588-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 04/17/2019] [Indexed: 12/11/2022] Open
Abstract
Myotonic dystrophy type 1 is a multisystem disorder caused by the expansion of a trinucleotide repeat in the DMPK gene. In this study we evaluated the performance of the FastDM1TMDMPK sizing kit in myotonic dystrophy type 1 testing. This commercially available triplet repeat-primed PCR based kit was validated using reference and clinical samples. Based on testing with 19 reference samples, the assay yielded repeat sizes within three repeats from the consensus reference length, demonstrating an accuracy of 100%. Additionally, the assay generated consistent repeat size information with a concentration range of template-DNA, and upon repetition and reproduction (CV 0.36% to 0.41%). Clinical performance was established with 235 archived prenatal and postnatal clinical samples, yielding results of 100% sensitivity (95% CI, 97.29% to 100%) and 100% specificity (95% CI, 96.19% to 100%) in classifying the samples into the respective genotype groups of 5–35 (normal), 36–50 (non-pathogenic pre-expansion), 51–150 (unstable intermediate-sized pathogenic) or >150 (unstable pathogenic) CTG repeats, respectively. Furthermore, the assay identified interrupted repeat expansions in all samples known to have interruptions, and also identified interruptions in a subset of the clinical samples.
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Affiliation(s)
- Maike Leferink
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | | | - Shiwei Cai
- The BioFactory Pte Ltd, Singapore, Republic of Singapore
| | - Minli Yeo
- The BioFactory Pte Ltd, Singapore, Republic of Singapore
| | - Jocelin Ho
- The BioFactory Pte Ltd, Singapore, Republic of Singapore
| | - Mulias Lian
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Republic of Singapore
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
| | - Samuel S Chong
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Republic of Singapore.,Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Republic of Singapore.,Department of Laboratory Medicine, National University Hospital, Singapore, Republic of Singapore
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands.
| | - Ming Guan
- The BioFactory Pte Ltd, Singapore, Republic of Singapore
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Zhao M, Cheah FS, Tan AS, Agarwal A, Chong SS. Robust PGT-M of Huntington disease combining triplet-primed PCR of the HTT CAG repeat with multi-microsatellite haplotyping. Reprod Biomed Online 2019. [DOI: 10.1016/j.rbmo.2019.03.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Tan VJ, Lian M, Faradz SMH, Winarni TI, Chong SS. A Single Common Assay for Robust and Rapid Fragile X Mental Retardation Syndrome Screening From Dried Blood Spots. Front Genet 2018; 9:582. [PMID: 30538724 PMCID: PMC6277581 DOI: 10.3389/fgene.2018.00582] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 11/08/2018] [Indexed: 12/24/2022] Open
Abstract
Background:FMR1 CGG trinucleotide repeat hyper-expansions are observed in 99% of individuals with fragile X mental retardation syndrome (FXS). We evaluated the reliability of a rapid single-step gender-neutral molecular screen for FXS when performed on DNA isolated from dried blood spots. Methods: DNA was extracted from dried blood spots of 151 individuals with intellectual disability or autism spectrum disorder, whose FMR1 repeat genotypes are known. Dried blood spots were blinded prior to DNA extraction and analysis by triplet primed PCR (TP-PCR) and melt curve analysis (MCA). All expansion-positive and representative expansion-negative samples were also genotyped by fluorescent TP-PCR and capillary electrophoresis (CE) to confirm repeat expansion status. Results: Three males and 12 females were classified as expanded by TP-PCR MCA, and were subsequently sized by fluorescent TP-PCR CE. Two males and four females carried premutations, while one male and eight females carried full mutations. All 19 non-expanded samples that were sized were confirmed as carrying only normal alleles. Replicate analysis of representative expansion-positive samples yielded reproducible melt peak profiles. TP-PCR MCA classifications were completely concordant with FMR1 CGG repeat genotypes. Conclusion: TP-PCR MCA of dried blood spot DNA accurately and reliably identifies presence/absence of FMR1 CGG repeat expansions in both genders simultaneously. This strategy may be suitable for rapid high-throughput first-tier screening for fragile X syndrome.
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Affiliation(s)
- Vivienne J Tan
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mulias Lian
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore
| | - Sultana M H Faradz
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Tri I Winarni
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
| | - Samuel S Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore, Singapore.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore, Singapore
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Zhao M, Cheah FSH, Chen M, Lee CG, Law HY, Chong SS. Improved high sensitivity screen for Huntington disease using a one-step triplet-primed PCR and melting curve assay. PLoS One 2017; 12:e0180984. [PMID: 28700716 PMCID: PMC5507316 DOI: 10.1371/journal.pone.0180984] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 05/22/2017] [Indexed: 11/19/2022] Open
Abstract
Molecular diagnosis of Huntington disease (HD) is currently performed by fluorescent repeat-flanking or triplet-primed PCR (TP-PCR) with capillary electrophoresis (CE). However, CE requires multiple post-PCR steps and may result in high cost in high-throughput settings. We previously described a cost-effective single-step molecular screening strategy employing the use of melting curve analysis (MCA). However, because it relies on repeat-flanking PCR, its efficiency in detecting expansion mutations decreases with increasing size of the repeat, which could lead to false-negative results. To address this pitfall, we have developed an improved screening assay coupling TP-PCR, which has been shown in CE-based assays to detect all expanded alleles regardless of size, with MCA in a rapid one-step assay. A companion protocol for rapid size confirmation of expansion-positive samples is also described. The assay was optimized on 30 genotype-known DNAs, and two plasmids pHTT(CAG)26 and pHTT(CAG)33 were used to establish the threshold temperatures (TTs) distinguishing normal from expansion-positive samples. In contrast to repeat-flanking PCR MCA, TP-PCR MCA displayed much higher sensitivity for detecting large expansions. All 30 DNAs generated distinct melt peak Tms which correlated well with each sample's larger allele. Normal samples were clearly distinguished from affected samples. The companion sizing protocol accurately sized even the largest expanded allele of ~180 CAGs. Blinded analysis of 69 clinical samples enriched for HD demonstrated 100% assay sensitivity and specificity in sample segregation. The assay targets the HTT CAG repeat specifically, tolerates a wide range of input DNA, and works well using DNA from saliva and buccal swab in addition to blood. Therefore, rapid, accurate, reliable, and high-throughput detection/exclusion of HD can be achieved using this one-step screening assay, at less than half the cost of fluorescent PCR with CE.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Felicia S. H. Cheah
- Khoo Teck Puat – National University Children’s Medical Institute, National University Health System, Singapore, Singapore
| | - Min Chen
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Caroline G. Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Division of Medical Sciences, National Cancer Center, Singapore, Singapore
- Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women’s and Children’s Hospital, Singapore, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat – National University Children’s Medical Institute, National University Health System, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
- * E-mail:
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Zhao M, Chen M, Tan ASC, Cheah FSH, Mathew J, Wong PC, Chong SS. Single-tube tetradecaplex panel of highly polymorphic microsatellite markers < 1 Mb from F8 for simplified preimplantation genetic diagnosis of hemophilia A. J Thromb Haemost 2017; 15:1473-1483. [PMID: 28345288 DOI: 10.1111/jth.13685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Indexed: 11/30/2022]
Abstract
Essentials Preimplantation genetic diagnosis (PGD) of severe hemophilia A relies on linkage analysis. Simultaneous multi-marker screening can simplify selection of informative markers in a couple. We developed a single-tube tetradecaplex panel of polymorphic markers for hemophilia A PGD use. Informative markers can be used for linkage analysis alone or combined with mutation detection. SUMMARY Background It is currently not possible to perform single-cell preimplantation genetic diagnosis (PGD) to directly detect the common inversion mutations of the factor VIII (F8) gene responsible for severe hemophilia A (HEMA). As such, PGD for such inversion carriers relies on indirect analysis of linked polymorphic markers. Objectives To simplify linkage-based PGD of HEMA, we aimed to develop a panel of highly polymorphic microsatellite markers located near the F8 gene that could be simultaneously genotyped in a multiplex-PCR reaction. Methods We assessed the polymorphism of various microsatellite markers located ≤ 1 Mb from F8 in 177 female subjects. Highly polymorphic markers were selected for co-amplification with the AMELX/Y indel dimorphism in a single-tube reaction. Results Thirteen microsatellite markers located within 0.6 Mb of F8 were successfully co-amplified with AMELX/Y in a single-tube reaction. Observed heterozygosities of component markers ranged from 0.43 to 0.84, and ∼70-80% of individuals were heterozygous for ≥ 5 markers. The tetradecaplex panel successfully identified fully informative markers in a couple interested in PGD for HEMA because of an intragenic F8 point mutation, with haplotype phasing established through a carrier daughter. In-vitro fertilization (IVF)-PGD involved single-tube co-amplification of fully informative markers with AMELX/Y and the mutation-containing F8 amplicon, followed by microsatellite analysis and amplicon mutation-site minisequencing analysis. Conclusions The single-tube multiplex-PCR format of this highly polymorphic microsatellite marker panel simplifies identification and selection of informative markers for linkage-based PGD of HEMA. Informative markers can also be easily co-amplified with mutation-containing F8 amplicons for combined mutation detection and linkage analysis.
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Affiliation(s)
- M Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - M Chen
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
| | - A S C Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore City, Singapore
| | - F S H Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore City, Singapore
| | - J Mathew
- Department of Obstetrics and Gynecology, Clinic for Human Reproduction, National University Health System, Singapore City, Singapore
| | - P C Wong
- Department of Obstetrics and Gynecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
- Department of Obstetrics and Gynecology, Clinic for Human Reproduction, National University Health System, Singapore City, Singapore
| | - S S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore City, Singapore
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore City, Singapore
- Department of Laboratory Medicine, National University Health System, Singapore City, Singapore
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Lian M, Zhao M, Lee CG, Chong SS. Single-Tube Dodecaplex PCR Panel of Polymorphic Microsatellite Markers Closely Linked to the DMPK CTG Repeat for Preimplantation Genetic Diagnosis of Myotonic Dystrophy Type 1. Clin Chem 2017; 63:1127-1140. [PMID: 28428361 DOI: 10.1373/clinchem.2017.271528] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/08/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Preimplantation genetic diagnosis (PGD) of myotonic dystrophy type 1 (DM1) currently uses conventional PCR to detect nonexpanded dystrophia myotonica protein kinase (DMPK) alleles or triplet-primed PCR to detect the CTG-expanded alleles, coupled with analysis of linked microsatellite markers to increase diagnostic accuracy. We aimed to simplify the process of identification and selection of informative linked markers for application to DM1 PGD. METHODS An in silico search was performed to identify all markers within 1-1.5 Mb flanking the DMPK gene. Five previously known (D19S559, APOC2, D19S543, D19S112, and BV209569) and 7 novel (DM45050, DM45178, DM45209, DM45958, DM46513, DM46892, and DM47004.1) markers with potentially high heterozygosity values and polymorphism information content were selected and optimized in a single-tube multiplex PCR panel. RESULTS Analysis of 184 DNA samples of Chinese and Caucasian individuals (91 from unrelated, anonymized cord blood of Chinese babies born at the National University Hospital, Singapore, and 93 Caucasian DNA samples from the Human Variation Panel HD100CAU) confirmed the high polymorphism indices of all markers (polymorphism information content >0.5), with observed heterozygosity values ranging from 0.62-0.93. All individuals were heterozygous for at least 6 markers, with 99.5% of individuals heterozygous for at least 2 markers on either side of the DMPK CTG repeat. The dodecaplex marker assay was successfully validated on 42 single cells and 12 whole genome amplified single cells. CONCLUSIONS The DM1 multiplex PCR panel is suitable for use in DM1 PGD either as a standalone linkage-based assay or as a complement to DMPK CTG repeat expansion-mutation detection.
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Affiliation(s)
- Mulias Lian
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore
| | | | - Caroline G Lee
- Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.,Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore.,Division of Medical Sciences, National Cancer Center, Singapore
| | - Samuel S Chong
- Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore; .,Departments of Pediatrics and.,Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore
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Lim GXY, Yeo M, Koh YY, Winarni TI, Rajan-Babu IS, Chong SS, Faradz SMH, Guan M. Validation of a commercially available test that enables the quantification of the numbers of CGG trinucleotide repeat expansion in FMR1 gene. PLoS One 2017; 12:e0173279. [PMID: 28278294 PMCID: PMC5344422 DOI: 10.1371/journal.pone.0173279] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 02/13/2017] [Indexed: 11/26/2022] Open
Abstract
In the present study, we evaluated a commercially available TP-PCR-based assay, the FastFraXTMFMR1 Sizing kit, as a test in quantifying the number of CGG repeats in the FMR1 gene. Based on testing with well characterized DNA samples from Coriell, the kit yielded size results within 3 repeats of those obtained by common consensus (n = 14), with the exception of one allele. Furthermore, based on data obtained using all Coriell samples with or without common consensus (n = 29), the Sizing kit was 97.5% in agreement with existing approaches. Additionally, the kit generated consistent size information in repeatability and reproducibility studies (CV 0.39% to 3.42%). Clinical performance was established with 198 archived clinical samples, yielding results of 100% sensitivity (95% CI, 91.03% to 100%) and 100% specificity (95% CI, 97.64% to 100%) in categorizing patient samples into the respective normal, intermediate, premutation and full mutation genotypes.
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Affiliation(s)
| | - Minli Yeo
- The BioFactory Pte Ltd, Singapore, Singapore
| | | | - Tri Indah Winarni
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Indhu-Shree Rajan-Babu
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Samuel S. Chong
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Sultana M. H. Faradz
- Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Ming Guan
- The BioFactory Pte Ltd, Singapore, Singapore
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Lim YC, Tan KM, Chong SS, Rajendran J, Sampath V. A Patient with β-Thalassemia Intermedia Secondary to Homozygosity for a Polyadenylation Signal Mutation (AATAAA > AATAGA) (HBB: C.*112A > G) on the β-Globin Gene. Hemoglobin 2016; 40:359-360. [DOI: 10.1080/03630269.2016.1237960] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yen-Chian Lim
- Department of Haematology, Tan Tock Seng Hospital, Singapore
| | - Karen M.L. Tan
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
| | - Samuel S. Chong
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Singapore
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University Singapore, Singapore
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Lian M, Law HY, Lee CG, Chong SS. Defining the performance parameters of a rapid screening tool for myotonic dystrophy type 1 based on triplet-primed PCR and melt curve analysis. Expert Rev Mol Diagn 2016; 16:1221-1232. [PMID: 27665623 DOI: 10.1080/14737159.2016.1241145] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
BACKGROUND DMPK CTG-repeat expansions that cause myotonic dystrophy type 1 (DM1) can be detected more rapidly, cost-effectively, and simply by combining triplet-primed PCR (TP-PCR) with melting curve analysis (MCA). We undertook a detailed technical validation study to define the optimal operational parameters for performing bidirectional TP-PCR MCA assays. METHODS We determined the assays' analytic specificity and sensitivity, assessed the effect of reaction volumes, DNA diluents, and common contaminants on melt peak temperature, determined the assays' sensitivity in detecting low-level mosaicism for repeat expansion, and evaluated their performance on two real-time PCR platforms. RESULTS Both assays were highly specific and sensitive, and performed optimally under a broad range of parameters. Bidirectional TP-PCR MCA analysis also reduces the risk of generating false-negative results associated with the rare CCG-interruptions that may be present at either end of expanded alleles. CONCLUSION The DMPK TP-PCR MCA is a highly specific, sensitive, and significantly cost-saving screening tool for DM1.
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Affiliation(s)
- Mulias Lian
- a Khoo Teck Puat - National University Children's Medical Institute , National University Health System , Singapore , Singapore
| | - Hai-Yang Law
- b Department of Pediatric Medicine , KK Women's and Children's Hospital , Singapore , Singapore.,c Pediatrics Academic Clinical Program , Duke-NUS Graduate Medical School , Singapore , Singapore
| | - Caroline G Lee
- d Department of Biochemistry, Yong Loo Lin School of Medicine , National University of Singapore , Singapore , Singapore.,e Cancer and Stem Cell Biology Program , Duke-NUS Graduate Medical School , Singapore , Singapore.,f Division of Medical Sciences , National Cancer Center , Singapore , Singapore
| | - Samuel S Chong
- a Khoo Teck Puat - National University Children's Medical Institute , National University Health System , Singapore , Singapore.,g Department of Pediatrics, Yong Loo Lin School of Medicine , National University of Singapore , Singapore , Singapore.,h Department of Laboratory Medicine , National University Hospital, National University Health System , Singapore , Singapore
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Rajan-Babu IS, Lian M, Tran AH, Dang TT, Le HTM, Thanh MN, Lee CG, Chong SS. Defining the Performance Parameters of a Rapid Screening Tool for FMR1 CGG-Repeat Expansions Based on Direct Triplet-Primed PCR and Melt Curve Analysis. J Mol Diagn 2016; 18:719-730. [DOI: 10.1016/j.jmoldx.2016.05.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 04/01/2016] [Accepted: 05/02/2016] [Indexed: 12/12/2022] Open
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Zhao M, Chen M, Lee CG, Chong SS. Identification of Novel Microsatellite Markers <1 Mb from the HTT CAG Repeat and Development of a Single-Tube Tridecaplex PCR Panel of Highly Polymorphic Markers for Preimplantation Genetic Diagnosis of Huntington Disease. Clin Chem 2016; 62:1096-105. [PMID: 27335079 DOI: 10.1373/clinchem.2016.255711] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 05/11/2016] [Indexed: 12/11/2022]
Abstract
BACKGROUND Preimplantation genetic diagnosis (PGD) of Huntington disease (HD) generally employs linkage analysis of flanking microsatellite markers to complement direct mutation testing, as well as for exclusion testing. Thus far, only 10 linked markers have been developed for use in HD PGD, with a maximum of 3 markers coamplified successfully. We aimed to develop a single-tube multiplex PCR panel of highly polymorphic markers to simplify HD PGD. METHODS An in silico search was performed to identify all markers within 1 Mb flanking the huntingtin (HTT) gene. Selected markers were optimized in a single-tube PCR panel, and their polymorphism indices were determined in 2 populations. The panel was tested on 63 single cells to validate its utility in PGD. RESULTS We identified 102 markers in silico, of which 56 satisfied the selection criteria. After initial testing, 12 markers with potentially high heterozygosity were optimized into a single-tube PCR panel together with a 13th more distally located marker. Analysis of DNA from 183 Chinese and Caucasian individuals revealed high polymorphism indices for all markers (polymorphism information content >0.5), with observed heterozygosities ranging from 0.5-0.92. All individuals were heterozygous for at least 5 markers, with 99.5% of individuals heterozygous for at least 2 markers upstream and downstream of the HTT CAG repeat. CONCLUSIONS The tridecaplex marker assay amplified reliably from single cells either directly or after whole genome amplification, thus validating its standalone use in HD exclusion PGD or as a complement to HTT CAG repeat expansion-mutation detection.
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Affiliation(s)
| | | | - Caroline G Lee
- Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Division of Medical Sciences, National Cancer Center, Singapore; Cancer and Stem Cell Biology Program, Duke-NUS Graduate Medical School, Singapore
| | - Samuel S Chong
- Departments of Pediatrics and Preimplantation Genetic Diagnosis Center, Khoo Teck Puat-National University Children's Medical Institute, National University Health System, Singapore; Molecular Diagnosis Center and Clinical Cytogenetics Service, Department of Laboratory Medicine, National University Hospital, National University Health System, Singapore.
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Zhao M, Lee CG, Law HY, Chong SS. Enhanced Detection and Sizing of the HTT CAG Repeat Expansion in Huntington Disease Using an Improved Triplet-Primed PCR Assay. NEURODEGENER DIS 2016; 16:348-51. [PMID: 27207688 DOI: 10.1159/000444714] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/16/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Accurate determination of the CAG repeat number is crucial for diagnostic and predictive testing for Huntington disease (HD). Current PCR-based assays can accurately size up to ∼110 HTT CAG repeats. OBJECTIVE To develop an improved assay capable of detecting larger CAG repeat expansions. METHODS A triplet-primed PCR (TP-PCR) assay was optimized and validated on 14 HD reference DNAs, including a sample carrying a large expansion of ∼180 CAG repeats. RESULTS All 14 HD reference samples showed 100% concordance with the previously verified allele sizes. For alleles under 45 CAGs, identical repeat sizes were obtained, while alleles larger than 46 CAGs were sized to within ±1 CAG. The improved TP-PCR assay successfully detected the ∼180 CAG repeat allele in an affected sample. CONCLUSION This method extends the detection limit of large expanded alleles to at least ∼175-180 CAG repeats, thus reducing the likelihood of requiring Southern blot analysis for any HD-affected sample.
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Affiliation(s)
- Mingjue Zhao
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
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Chen M, Tan ASC, Cheah FSH, Saw EEL, Chong SS. Identification of novel microsatellite markers <1 Mb from theHBBgene and development of a single-tube pentadecaplex PCR panel of highly polymorphic markers for preimplantation genetic diagnosis of beta-thalassemia. Electrophoresis 2015; 36:2914-24. [DOI: 10.1002/elps.201500146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/20/2015] [Accepted: 08/17/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Min Chen
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
| | - Arnold S. C. Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Felicia S. H. Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Eugene E. L. Saw
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Department of Laboratory Medicine; National University Hospital; Singapore
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Chen M, Loh SF, Yu SL, Nair S, Tan HH, Nadarajah S, Wong PC, Ng SC, Prasath EB, Tan AS, Cheah FS, Saw EE, Chong SS. Rapid and reliable preimplantation genetic diagnosis of common hemoglobin Bart's hydrops fetalis syndrome and hemoglobin H disease determinants using an enhanced single-tube decaplex polymerase chain reaction assay. Am J Hematol 2015; 90:E194-6. [PMID: 26043722 DOI: 10.1002/ajh.24077] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 05/22/2015] [Accepted: 05/27/2015] [Indexed: 12/20/2022]
Affiliation(s)
- Min Chen
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Khoo Teck Puat-National University Children's Medical Institute, National University Health System; Singapore
| | - Seong Feei Loh
- Thomson Fertility Centre; Thomson Medical Centre; Singapore
| | - Su Ling Yu
- Centre for Assisted Reproduction, Department of Obstetrics & Gynaecology; Singapore General Hospital; Singapore
| | - Suresh Nair
- Gynecology Consultants Clinic and Surgery; Singapore
| | - Heng Hao Tan
- KKIVF, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Sadhana Nadarajah
- KKIVF, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Peng-Cheang Wong
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology; National University Hospital; Singapore
| | - Soon Chye Ng
- Sincere IVF Center, Sincere Healthcare Group; Singapore
| | | | - Arnold S.C. Tan
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Preimplantation Genetic Diagnosis Center; Khoo Teck Puat - National University Children's Medical Institute, National University Health System; Singapore
| | - Felicia S.H. Cheah
- Preimplantation Genetic Diagnosis Center; Khoo Teck Puat - National University Children's Medical Institute, National University Health System; Singapore
| | - Eugene E.L. Saw
- Preimplantation Genetic Diagnosis Center; Khoo Teck Puat - National University Children's Medical Institute, National University Health System; Singapore
| | - Samuel S. Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine; National University of Singapore; Singapore
- Preimplantation Genetic Diagnosis Center; Khoo Teck Puat - National University Children's Medical Institute, National University Health System; Singapore
- Department of Laboratory Medicine; National University Hospital; Singapore
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Bu L, Chen Q, Wang H, Zhang T, Hetmanski JB, Schwender H, Parker M, Chou YHW, Yeow V, Chong SS, Zhang B, Jabs EW, Scott AF, Beaty TH. Novel evidence of association with nonsyndromic cleft lip with or without cleft palate was shown for single nucleotide polymorphisms in FOXF2 gene in an Asian population. ACTA ACUST UNITED AC 2015; 103:857-62. [PMID: 26278207 DOI: 10.1002/bdra.23413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 06/15/2015] [Accepted: 06/28/2015] [Indexed: 11/07/2022]
Abstract
BACKGROUND The forkhead box F2 gene (FOXF2) located in chromosome 6p25.3 has been shown to play a crucial role in palatal development in mouse and rat models. To date, no evidence of linkage or association has been reported for this gene in humans with oral clefts. METHODS Allelic transmission disequilibrium tests were used to robustly assess evidence of linkage and association with nonsyndromic cleft lip with or without cleft palate for nine single nucleotide polymorphisms (SNPs) in and around FOXF2 in both Asian and European trios using PLINK. RESULTS Statistically significant evidence of linkage and association was shown for two SNPs (rs1711968 and rs732835) in 216 Asian trios where the empiric P values with permutation tests were 0.0016 and 0.005, respectively. The corresponding estimated odds ratios for carrying the minor allele at these SNPs were 2.05 (95% confidence interval = 1.41, 2.98) and 1.77 (95% confidence interval = 1.26, 2.49), respectively. CONCLUSION Our results provided statistical evidence of linkage and association between FOXF2 and nonsyndromic cleft lip with or without cleft palate.
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Affiliation(s)
- Lingxue Bu
- Department of Oral and Maxillofacial Surgery, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Qianqian Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,National Center for Public Health Surveillance and Information Services, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China.,Ministry of Health KeyLaboratory of Reproductive Health, Beijing, China
| | - Tianxiao Zhang
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri
| | - Jacqueline B Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Margaret Parker
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Yah-Huei Wu Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taipei, Taiwan
| | - Vincent Yeow
- Department of Plastic Surgery, K K Women's and Children's Hospital, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Khoo Teck Puat - National University Children's Medical Institute, National University Health System, Singapore
| | - Bo Zhang
- Department of Biomedical Engineering, Xi'an JiaoTong University, Xi'an, China
| | - Ethylin Wang Jabs
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA. Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Terri H Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Chen M, Chan JKY, Nadarajah S, Tan ASC, Chan MLH, Mathew J, Saw EEL, Lim C, Wong W, Cheah FSH, Law HY, Wong PC, Chong SS. Single-tube nonaplex microsatellite PCR panel for preimplantation genetic diagnosis of Hb Bart's hydrops fetalis syndrome. Prenat Diagn 2015; 35:534-43. [DOI: 10.1002/pd.4568] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Revised: 01/19/2015] [Accepted: 01/25/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Min Chen
- Yong Loo Lin School of Medicine, Department of Pediatrics; National University of Singapore; Singapore
| | - Jerry K. Y. Chan
- KKIVF Center, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Sadhana Nadarajah
- KKIVF Center, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Arnold S. C. Tan
- Yong Loo Lin School of Medicine, Department of Pediatrics; National University of Singapore; Singapore
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Melinda L. H. Chan
- KKIVF Center, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Joyce Mathew
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology; National University Hospital; Singapore
| | - Eugene E. L. Saw
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Cheryl Lim
- KKIVF Center, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Wendy Wong
- KKIVF Center, Department of Reproductive Medicine; KK Women's and Children's Hospital; Singapore
| | - Felicia S. H. Cheah
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
| | - Hai-Yang Law
- Department of Paediatric Medicine; KK Women's and Children's Hospital; Singapore
- Paediatrics Academic Clinical Program; Duke-NUS Graduate Medical School; Singapore
| | - Peng-Cheang Wong
- Clinic for Human Reproduction, Department of Obstetrics and Gynecology; National University Hospital; Singapore
| | - Samuel S. Chong
- Yong Loo Lin School of Medicine, Department of Pediatrics; National University of Singapore; Singapore
- Preimplantation Genetic Diagnosis Center, Khoo Teck Puat - National University Children's Medical Institute; National University Health System; Singapore
- Department of Laboratory Medicine; National University Hospital; Singapore
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Rajan-Babu IS, Teo CRL, Lian M, Lee CG, Law HY, Chong SS. Single-tube methylation-specific duplex-PCR assay for rapid and accurate diagnosis ofFragile X Mental Retardation 1–related disorders. Expert Rev Mol Diagn 2015; 15:431-41. [DOI: 10.1586/14737159.2015.1001749] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Wu T, Schwender H, Ruczinski I, Murray JC, Marazita ML, Munger RG, Hetmanski JB, Parker MM, Wang P, Murray T, Taub M, Li S, Redett RJ, Fallin MD, Liang KY, Wu-Chou YH, Chong SS, Yeow V, Ye X, Wang H, Huang S, Jabs EW, Shi B, Wilcox AJ, Jee SH, Scott AF, Beaty TH. Evidence of gene-environment interaction for two genes on chromosome 4 and environmental tobacco smoke in controlling the risk of nonsyndromic cleft palate. PLoS One 2014; 9:e88088. [PMID: 24516586 PMCID: PMC3916361 DOI: 10.1371/journal.pone.0088088] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 01/06/2014] [Indexed: 11/18/2022] Open
Abstract
Nonsyndromic cleft palate (CP) is one of the most common human birth defects and both genetic and environmental risk factors contribute to its etiology. We conducted a genome-wide association study (GWAS) using 550 CP case-parent trios ascertained in an international consortium. Stratified analysis among trios with different ancestries was performed to test for GxE interactions with common maternal exposures using conditional logistic regression models. While no single nucleotide polymorphism (SNP) achieved genome-wide significance when considered alone, markers in SLC2A9 and the neighboring WDR1 on chromosome 4p16.1 gave suggestive evidence of gene-environment interaction with environmental tobacco smoke (ETS) among 259 Asian trios when the models included a term for GxE interaction. Multiple SNPs in these two genes were associated with increased risk of nonsyndromic CP if the mother was exposed to ETS during the peri-conceptual period (3 months prior to conception through the first trimester). When maternal ETS was considered, fifteen of 135 SNPs mapping to SLC2A9 and 9 of 59 SNPs in WDR1 gave P values approaching genome-wide significance (10(-6)<P<10(-4)) in a test for GxETS interaction. SNPs rs3733585 and rs12508991 in SLC2A9 yielded P = 2.26×10(-7) in a test for GxETS interaction. SNPs rs6820756 and rs7699512 in WDR1 also yielded P = 1.79×10(-7) and P = 1.98×10(-7) in a 1 df test for GxE interaction. Although further replication studies are critical to confirming these findings, these results illustrate how genetic associations for nonsyndromic CP can be missed if potential GxE interaction is not taken into account, and this study suggest SLC2A9 and WDR1 should be considered as candidate genes for CP.
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Affiliation(s)
- Tao Wu
- Peking University Health Science Center, Beijing, China
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- * E-mail:
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Ingo Ruczinski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Jeffrey C. Murray
- University of Iowa, Children’s Hospital, Iowa City, Iowa, United States of America
| | - Mary L. Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | | | - Jacqueline B. Hetmanski
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret M. Parker
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Ping Wang
- Peking University Health Science Center, Beijing, China
| | - Tanda Murray
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Margaret Taub
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Shuai Li
- Peking University Health Science Center, Beijing, China
| | - Richard J. Redett
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - M. Daniele Fallin
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
| | - Kung Yee Liang
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
- National Yang-Ming University, Taipei, Taiwan
| | | | | | - Vincent Yeow
- KK Women’s & Children’s Hospital, Singapore, Singapore
| | - Xiaoqian Ye
- Wuhan University, School of Stomatology, Wuhan, China
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Hong Wang
- Peking University Health Science Center, Beijing, China
| | | | - Ethylin W. Jabs
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
- Mount Sinai Medical Center, New York, New York, United States of America
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Allen J. Wilcox
- NIEHS/NIH, Epidemiology Branch, Durham, North Carolina, United States of America
| | - Sun Ha Jee
- Yonsei University, School of Public Health, Seoul, Korea
| | - Alan F. Scott
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Johns Hopkins University, School of Public Health, Baltimore, Maryland, United States of America
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Teo CRL, Rajan-Babu IS, Law HY, Lee CG, Chong SS. Methylation-specific triplet-primed PCR and melting curve analysis as a rapid screening tool for identifying actionable FMR1 genotypes. Clin Chem 2013; 59:1668-70. [PMID: 24009158 DOI: 10.1373/clinchem.2013.206771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Yap ZM, Sun KM, Teo CR, Tan AS, Chong SS. Evidence of differential selection for the −α3.7and −α4.2single-α-globin gene deletions within the same population. Eur J Haematol 2013; 90:210-3. [DOI: 10.1111/ejh.12058] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/12/2012] [Indexed: 11/27/2022]
Affiliation(s)
- Zhi Min Yap
- University College London Medical School; University College London; London; UK
| | - Kar Mun Sun
- School of Biological Sciences; Nanyang Technological University of Singapore; Singapore
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Loh SF, Wong PC, Jiang B, Yeo GH, Tan ASC, Prasath EB, Mathew J, Chan MLH, Tan WC, Choolani M, Yap CHA, Chong SS. Preimplantation genetic diagnosis of chromosome translocations by analysis of polymorphic short tandem repeats. Singapore Med J 2012; 53:648-654. [PMID: 23112015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
INTRODUCTION We aimed to develop and implement a short tandem repeat (STR) polymerase chain reaction alternative to fluorescence in situ hybridisation (FISH) for the preimplantation genetic diagnosis (PGD) of chromosomal translocations. METHODS Selected informative STRs located on translocated arms of relevant chromosomes were used to discriminate between normal and unbalanced chromosome states in each embryo. RESULTS PGD cycles were performed on five couples where one spouse carried a balanced translocation. 27 embryos were analysed, of which 12 were normal/balanced, 12 were abnormal/unbalanced and three were indeterminate. Four PGD cycles proceeded to embryo transfer, of which two led to pregnancy. The first pregnancy showed a normal male karyotype, and a healthy baby was delivered at term. A second pregnancy unexpectedly miscarried in the second trimester from unknown causes. CONCLUSION STR analysis is a simple and suitable alternative to FISH for detecting unbalanced chromosomal states in preimplantation embryos.
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Affiliation(s)
- Seong Feei Loh
- KKIVF, Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore
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Wang J, S.Y. Pang G, S. Chong S, G.L. Lee C. SNP Web Resources and Their Potential Applications in Personalized Medicine. Curr Drug Metab 2012; 13:978-90. [DOI: 10.2174/138920012802138552] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 04/25/2011] [Accepted: 05/03/2011] [Indexed: 11/22/2022]
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Chen Q, Wang H, Hetmanski JB, Zhang T, Ruczinski I, Schwender H, Liang KY, Fallin MD, Redett RJ, Raymond GV, Wu Chou YH, Chen PKT, Yeow V, Chong SS, Cheah FSH, Jabs EW, Scott AF, Beaty TH. BMP4 was associated with NSCL/P in an Asian population. PLoS One 2012; 7:e35347. [PMID: 22514733 PMCID: PMC3325933 DOI: 10.1371/journal.pone.0035347] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Accepted: 03/14/2012] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND The Bone Morphogenetic Protein 4 gene (BMP4) is located in chromosome 14q22-q23 which has shown evidence of linkage for isolated nonsyndromic cleft lip with or without cleft palate (NSCL/P) in a genome wide linkage analysis of human multiplex families. BMP4 has been shown to play crucial roles in lip and palatal development in animal models. Several candidate gene association analyses also supported its potential risk for NSCL/P, however, results across these association studies have been inconsistent. The aim of the current study was to test for possible association between markers in and around the BMP4 gene and NSCL/P in Asian and Maryland trios. METHODOLOGY/PRINCIPAL FINDINGS Family Based Association Test was used to test for deviation from Mendelian assortment for 12 SNPs in and around BMP4. Nominal significant evidence of linkage and association was seen for three SNPs (rs10130587, rs2738265 and rs2761887) in 221 Asian trios and for one SNP (rs762642) in 76 Maryland trios. Statistical significance still held for rs10130587 after Bonferroni correction (corrected p = 0.019) among the Asian group. Estimated odds ratio for carrying the apparent high risk allele at this SNP was 1.61 (95%CI = 1.20, 2.18). CONCLUSIONS Our results provided further evidence of association between BMP4 and NSCL/P.
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Affiliation(s)
- Qianqian Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, China
| | - Jacqueline B. Hetmanski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Tianxiao Zhang
- Division of Biology and Biomedical Sciences, Washington University, St. Louis, Missouri, United States of America
| | - Ingo Ruczinski
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Holger Schwender
- Department of Faculty of Statistics, TU Dortmund University, Dortmund, Germany
| | - Kung Yee Liang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - M. Daniele Fallin
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Richard J. Redett
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Gerald V. Raymond
- Kennedy Krieger Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yah-Huei Wu Chou
- Department of Medical Research, Chang Gung Memorial Hospital, Taipei, Taiwan
| | | | - Vincent Yeow
- Department of Plastic Surgery, K K Women's and Children's Hospital, Singapore, Singapore
| | - Samuel S. Chong
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Felicia S. H. Cheah
- Department of Pediatrics, National University of Singapore, Singapore, Singapore
| | - Ethylin Wang Jabs
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York City, New York, United States of America
| | - Alan F. Scott
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Terri H. Beaty
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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Shi M, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Wu T, Murray T, Redett RJ, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Yeow V, Chong SS, Shi B, Christensen K, Scott AF, Patel P, Cheah F, Beaty TH. Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts. Am J Med Genet A 2012; 158A:784-94. [PMID: 22419666 DOI: 10.1002/ajmg.a.35257] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 12/19/2011] [Indexed: 12/15/2022]
Abstract
We performed a genome wide association analysis of maternally-mediated genetic effects and parent-of-origin (POO) effects on risk of orofacial clefting (OC) using over 2,000 case-parent triads collected through an international cleft consortium. We used log-linear regression models to test individual SNPs. For SNPs with a P-value <10(-5) for maternal genotypic effects, we also applied a haplotype-based method, TRIMM, to extract potential information from clusters of correlated SNPs. None of the SNPs were significant at the genome wide level. Our results suggest neither maternal genome nor POO effects play major roles in the etiology of OC in our sample. This finding is consistent with previous genetic studies and recent population-based cohort studies in Norway and Denmark, which showed no apparent difference between mother-to-offspring and father-to-offspring recurrence of clefting. We, however, cannot completely rule out maternal genome or POO effects as risk factors because very small effects might not be detectable with our sample size, they may influence risk through interactions with environmental exposures or may act through a more complex network of interacting genes. Thus, the most promising SNPs identified by this study may still be worth further investigation.
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Affiliation(s)
- Min Shi
- Biostatistics Branch, NIEHS/NIH, Durham, North Carolina, USA.
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Teo CRL, Law HY, Lee CG, Chong SS. Screening for CGG Repeat Expansion in the FMR1 Gene by Melting Curve Analysis of Combined 5′ and 3′ Direct Triplet-Primed PCRs. Clin Chem 2012; 58:568-79. [DOI: 10.1373/clinchem.2011.174615] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Abstract
BACKGROUND
CGG repeat expansions in the FMR1 (fragile X mental retardation 1) gene are associated with fragile X syndrome, fragile X–associated tremor/ataxia syndrome, and fragile X–associated primary ovarian insufficiency. We evaluated the use of melting curve analysis (MCA) of triplet-primed PCR (TP-PCR) assays as a rapid screening tool for the positive identification of expanded FMR1 alleles in men and women.
METHODS
Both 5′- and 3′-weighted direct TP-PCRs (dTP-PCRs) were evaluated on 29 cell line–derived DNA samples and 44 blinded clinical samples. The presence of expansions was identified by the melting curve profiles generated automatically through MCA on the LightCycler 480 Real-Time PCR System. All samples were also analyzed by capillary electrophoresis to confirm the identities of the PCR fragments that gave rise to the observed melt peak profiles.
RESULTS
The presence of expanded alleles in samples from both males and females produced melt peak profiles that were distinct from those of individuals with the normal allelic form. In the blinded test, positive and negative calls for the presence of an expanded allele corroborated with previously determined genotype classifications for all samples.
CONCLUSIONS
The approach of dTP-PCR plus MCA offers a single-step strategy with high diagnostic sensitivity and specificity for rapid screening detection of FMR1 CGG repeat expansions, regardless of sex. The combined use of 5′- and 3′-weighted dTP-PCR assays minimizes the incidence of false-negative results arising from repeat-flanking deletions.
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Affiliation(s)
- Clara R L Teo
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Hai-Yang Law
- Department of Pediatric Medicine, KK Women's and Children's Hospital, Singapore
| | - Caroline G Lee
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Division of Medical Sciences, National Cancer Center, Singapore
- Duke-NUS Graduate Medical School, Singapore
| | - Samuel S Chong
- Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- University Children's Medical Institute and
- Department of Laboratory Medicine, National University Hospital, Singapore
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Wang H, Hetmanski JB, Ruczinski I, Liang KY, Fallin MD, Redett RJ, Raymond GV, Chou YHW, Chen PKT, Yeow V, Chong SS, Cheah FS, Jabs EW, Scott AF, Beaty TH. ROR2 gene is associated with risk of non-syndromic cleft palate in an Asian population. Chin Med J (Engl) 2012; 125:476-480. [PMID: 22490406 PMCID: PMC3384720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND The receptor tyrosine kinase-like orphan receptor 2 (ROR2) gene has been recently shown to play important roles in palatal development in animal models and resides in the chromosomal region linked to non syndromic cleft lip with or without cleft palate in humans. The aim of this study was to investigate the possible association between ROR2 gene and non-syndromic oral clefts. METHODS Here we tested 38 eligible single-nucleotide polymorphisms (SNPs) in ROR2 gene in 297 non-syndromic cleft lip with or without cleft palate and in 82 non-syndromic cleft palate case parent trios recruited from Asia and Maryland. Family Based Association Test was used to test for deviation from Mendelian inheritance. Plink software was used to test potential parent of origin effect. Possible maternally mediated in utero effects were assessed using the TRIad Multi-Marker approach under an assumption of mating symmetry in the population. RESULTS Significant evidence of linkage and association was shown for 3 SNPs (rs7858435, rs10820914 and rs3905385) among 57 Asian non-syndromic cleft palate trios in Family Based Association Tests. P values for these 3 SNPs equaled to 0.000068, 0.000115 and 0.000464 respectively which were all less than the significance level (0.05/38 = 0.0013) adjusted by strict Bonferroni correction. Relevant odds ratios for the risk allele were 3.42 (1.80 - 6.50), 3.45 (1.75 - 6.67) and 2.94 (1.56 - 5.56), respectively. Statistical evidence of linkage and association was not shown for study groups other than non-syndromic cleft palate. Neither evidence for parent-of-origin nor maternal genotypic effect was shown for any of the ROR2 markers in our analysis for all study groups. CONCLUSION Our results provided evidence of linkage and association between the ROR2 gene and a gene controlling risk to non-syndromic cleft palate.
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Affiliation(s)
- Hong Wang
- Department of Epidemiology and Biostatistics, Peking University School of Public Health, Beijing 100191, China.
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Wang J, Ronaghi M, Chong SS, Lee CGL. pfSNP: An integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses. Hum Mutat 2011; 32:19-24. [PMID: 20672376 DOI: 10.1002/humu.21331] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Currently, >14,000,000 single nucleotide polymorphisms (SNPs) are reported. Identifying phenotype-affecting SNPs among these many SNPs pose significant challenges. Although several Web resources are available that can inform about the functionality of SNPs, these resources are mainly annotation databases and are not very comprehensive. In this article, we present a comprehensive, well-annotated, integrated pfSNP (potentially functional SNPs) Web resource (http://pfs.nus.edu.sg/), which is aimed to facilitate better hypothesis generation through knowledge syntheses mediated by better data integration and a user-friendly Web interface. pfSNP integrates >40 different algorithms/resources to interrogate >14,000,000 SNPs from the dbSNP database for SNPs of potential functional significance based on previous published reports, inferred potential functionality from genetic approaches as well as predicted potential functionality from sequence motifs. Its query interface has the user-friendly "auto-complete, prompt-as-you-type" feature and is highly customizable, facilitating different combination of queries using Boolean-logic. Additionally, to facilitate better understanding of the results and aid in hypotheses generation, gene/pathway-level information with text clouds highlighting enriched tissues/pathways as well as detailed-related information are also provided on the results page. Hence, the pfSNP resource will be of great interest to scientists focusing on association studies as well as those interested to experimentally address the functionality of SNPs.
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Affiliation(s)
- Jingbo Wang
- Department of Biochemistry Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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