1
|
Xu D, Mao A, Chen L, Wu L, Ma Y, Mei C. Comprehensive Analysis of PKD1 and PKD2 by Long-Read Sequencing in Autosomal Dominant Polycystic Kidney Disease. Clin Chem 2024; 70:841-854. [PMID: 38527221 DOI: 10.1093/clinchem/hvae030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/23/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Autosomal dominant polycystic kidney disease (ADPKD) is mainly caused by heterogeneous variants in the PKD1 and PKD2 genes. Genetic analysis of PKD1 has been challenging due to homology with 6 PKD1 pseudogenes and high GC content. METHODS A single-tube multiplex long-range-PCR and long-read sequencing-based assay termed "comprehensive analysis of ADPKD" (CAPKD) was developed and evaluated in 170 unrelated patients by comparing to control methods including next-generation sequencing (NGS) and multiplex ligation-dependent probe amplification. RESULTS CAPKD achieved highly specific analysis of PKD1 with a residual noise ratio of 0.05% for the 6 pseudogenes combined. CAPKD identified PKD1 and PKD2 variants (ranging from variants of uncertain significance to pathogenic) in 160 out of the 170 patients, including 151 single-nucleotide variants (SNVs) and insertion-deletion variants (indels), 6 large deletions, and one large duplication. Compared to NGS, CAPKD additionally identified 2 PKD1 variants (c.78_96dup and c.10729_10732dup). Overall, CAPKD increased the rate of variant detection from 92.9% (158/170) to 94.1% (160/170), and the rate of diagnosis with pathogenic or likely pathogenic variants from 82.4% (140/170) to 83.5% (142/170). CAPKD also directly determined the cis-/trans-configurations in 11 samples with 2 or 3 SNVs/indels, and the breakpoints of 6 large deletions and one large duplication, including 2 breakpoints in the intron 21 AG-repeat of PKD1, which could only be correctly characterized by aligning to T2T-CHM13. CONCLUSIONS CAPKD represents a comprehensive and specific assay toward full characterization of PKD1 and PKD2 variants, and improves the genetic diagnosis for ADPKD.
Collapse
Affiliation(s)
- Dechao Xu
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Aiping Mao
- Department of Third-Generation Sequencing, Berry Genomics Corporation, Beijing, China
| | - Libao Chen
- Department of Third-Generation Sequencing, Berry Genomics Corporation, Beijing, China
| | - Le Wu
- Department of Third-Generation Sequencing, Berry Genomics Corporation, Beijing, China
| | - Yiyi Ma
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Changlin Mei
- Department of Nephrology, Changzheng Hospital, Naval Medical University, Shanghai, China
| |
Collapse
|
2
|
Wang N, Jiao K, He J, Zhu B, Cheng N, Sun J, Chen L, Chen W, Gong L, Qiao K, Xi J, Wu Q, Zhao C, Zhu W. Diagnosis of Challenging Spinal Muscular Atrophy Cases with Long-Read Sequencing. J Mol Diagn 2024; 26:364-373. [PMID: 38490302 DOI: 10.1016/j.jmoldx.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/17/2024] [Accepted: 02/07/2024] [Indexed: 03/17/2024] Open
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder primarily caused by the deletion or mutation of the survival motor neuron 1 (SMN1) gene. This study assesses the diagnostic potential of long-read sequencing (LRS) in three patients with SMA. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of multiplex ligation-dependent probe amplification, LRS, and PCR across the breakpoint. The third patient, born to a consanguineous family, bore four copies of hybrid SMN genes. LRS determined the genomic structures, indicating two distinct hybrids of SMN2 exon 7 and SMN1 exon 8. However, a discrepancy was found between the SMN1/SMN2 ratio interpretations by LRS (0:2) and multiplex ligation-dependent probe amplification (0:4), which suggested a limitation of LRS in SMA diagnosis. In conclusion, this newly adapted long PCR-based third-generation sequencing introduces an additional avenue for SMA diagnosis.
Collapse
Affiliation(s)
- Ningning Wang
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kexin Jiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jin He
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Bochen Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Nachuan Cheng
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jian Sun
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lan Chen
- Department of Neurology, Nantong First People's Hospital, Nantong, China
| | - Wanjin Chen
- Department of Neurology and Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Lingyun Gong
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Kai Qiao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianying Xi
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qihan Wu
- Shanghai Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, National Health Commission Key Lab of Reproduction Regulation, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Chongbo Zhao
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wenhua Zhu
- Department of Neurology, Huashan Hospital, Fudan University, Shanghai, China; National Center for Neurological Disorders, Shanghai, China; Huashan Rare Disease Center, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China.
| |
Collapse
|
3
|
Yao M, Jiang L, Yu Y, Cui Y, Chen Y, Zhou D, Gao F, Mao S. Optimized MLPA workflow for spinal muscular atrophy diagnosis: identification of a novel variant, NC_000005.10:g.(70919941_70927324)del in isolated exon 1 of SMN1 gene through long-range PCR. BMC Neurol 2024; 24:93. [PMID: 38468256 PMCID: PMC10926642 DOI: 10.1186/s12883-024-03592-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/13/2024] Open
Abstract
BACKGROUND Spinal muscular atrophy (SMA) is a rare autosomal recessive hereditary neuromuscular disease caused by survival motor neuron 1 (SMN1) gene deletion or mutation. Homozygous deletions of exon 7 in SMN1 result in 95% of SMA cases, while the remaining 5% are caused by other pathogenic variants of SMN1. METHODS We analyzed two SMA-suspected cases that were collected, with no SMN1 gene deletion and point mutation in whole-exome sequencing. Exon 1 deletion of the SMN gene was detected using Multiplex ligation-dependent probe amplification (MLPA) P021. We used long-range polymerase chain reaction (PCR) to isolate the SMN1 template, optimized-MLPA P021 for copy number variation (CNV) analysis within SMN1 only, and validated the findings via third-generation sequencing. RESULTS Two unrelated families shared a genotype with one copy of exon 7 and a novel variant, g.70919941_70927324del, in isolated exon 1 of the SMN1 gene. Case F1-II.1 demonstrated no exon 1 but retained other exons, whereas F2-II.1 had an exon 1 deletion in a single SMN1 gene. The read coverage in the third-generation sequencing results of both F1-II.1 and F2-II.1 revealed a deletion of approximately 7.3 kb in the 5' region of SMN1. The first nucleotide in the sequence data aligned to the 7385 bp of NG_008691.1. CONCLUSION Remarkably, two proband families demonstrated identical SMN1 exon 1 breakpoint sites, hinting at a potential novel mutation hotspot in Chinese SMA, expanding the variation spectrum of the SMN1 gene and corroborating the specificity of isolated exon 1 deletion in SMA pathogenesis. The optimized-MLPA P021 determined a novel variant (g.70919941_70927324del) in isolated exon 1 of the SMN1 gene based on long-range PCR, enabling efficient and affordable detection of SMN gene variations in patients with SMA, providing new insight into SMA diagnosis to SMN1 deficiency and an optimized workflow for single exon CNV testing of the SMN gene.
Collapse
Affiliation(s)
- Mei Yao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
- Department of Infectious Diseases, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Liya Jiang
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yicheng Yu
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yiqin Cui
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Yuwei Chen
- Xiamen Biofast Biotechnology Co., Ltd., Xiamen, China
| | - Dongming Zhou
- Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, China
| | - Feng Gao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China
| | - Shanshan Mao
- Department of Neurology, Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, 310052, China.
| |
Collapse
|
4
|
Xu Z, Hu L, Liu Y, Peng C, Zeng G, Zeng L, Yang M, Linpeng S, Bu X, Jiang X, Xie T, Chen L, Zhou S, He J. Comparison of Third-Generation Sequencing and Routine Polymerase Chain Reaction in Genetic Analysis of Thalassemia. Arch Pathol Lab Med 2024; 148:336-344. [PMID: 37270807 DOI: 10.5858/arpa.2022-0299-oa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2023] [Indexed: 06/06/2023]
Abstract
CONTEXT.— Thalassemia is the most widely distributed monogenic autosomal recessive disorder in the world. Accurate genetic analysis of thalassemia is crucial for thalassemia prevention. OBJECTIVE.— To compare the clinical utility of a third-generation sequencing-based approach termed comprehensive analysis of thalassemia alleles with routine polymerase chain reaction (PCR) in genetic analysis of thalassemia and explore the molecular spectrum of thalassemia in Hunan Province. DESIGN.— Subjects in Hunan Province were recruited, and hematologic testing was performed. Five hundred four subjects positive on hemoglobin testing were then used as the cohort, and third-generation sequencing and routine PCR were used for genetic analysis. RESULTS.— Of the 504 subjects, 462 (91.67%) had the same results, whereas 42 (8.33%) exhibited discordant results between the 2 methods. Sanger sequencing and PCR testing confirmed the results of third-generation sequencing. In total, third-generation sequencing correctly detected 247 subjects with variants, whereas PCR identified 205, which showed an increase in detection of 20.49%. Moreover, α triplications were identified in 1.98% (10 of 504) hemoglobin testing-positive subjects in Hunan Province. Seven hemoglobin variants with potential pathogenicity were detected in 9 hemoglobin testing-positive subjects. CONCLUSIONS.— Third-generation sequencing is a more comprehensive, reliable, and efficient approach for genetic analysis of thalassemia than PCR, and allowed for a characterization of the thalassemia spectrum in Hunan Province.
Collapse
Affiliation(s)
- Zhen Xu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Lanping Hu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Yinyin Liu
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Can Peng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Guo Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Li Zeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Mengyue Yang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Siyuan Linpeng
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xiufen Bu
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Xuanyu Jiang
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Tiantian Xie
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Libao Chen
- Berry Genomics Corporation, Beijing, China (Liu, Xie, Chen)
| | - Shihao Zhou
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| | - Jun He
- From the Department of Genetics and Eugenics, Changsha Hospital for Maternal & Child Health Care Affiliated to Hunan Normal University, Changsha, China (Xu, Hu, Peng, G. Zeng, L. Zeng, Yang, Linpeng, Bu, Jiang, Zhou, He)
| |
Collapse
|
5
|
Kiselev A, Maretina M, Shtykalova S, Al-Hilal H, Maslyanyuk N, Plokhih M, Serebryakova E, Frolova M, Shved N, Krylova N, Il’ina A, Freund S, Osinovskaya N, Sultanov I, Egorova A, Lobenskaya A, Koroteev A, Sosnina I, Gorelik Y, Bespalova O, Baranov V, Kogan I, Glotov A. Establishment of a Pilot Newborn Screening Program for Spinal Muscular Atrophy in Saint Petersburg. Int J Neonatal Screen 2024; 10:9. [PMID: 38390973 PMCID: PMC10885106 DOI: 10.3390/ijns10010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/24/2024] Open
Abstract
Spinal muscular atrophy 5q (SMA) is one of the most common neuromuscular inherited diseases and is the most common genetic cause of infant mortality. SMA is associated with homozygous deletion of exon 7 in the SMN1 gene. Recently developed drugs can improve the motor functions of infants with SMA when they are treated in the pre-symptomatic stage. With aim of providing an early diagnosis, newborn screening (NBS) for SMA using a real-time PCR assay with dried blood spots (DBS) was performed from January 2022 through November 2022 in Saint Petersburg, which is a representative Russian megapolis. Here, 36,140 newborns were screened by the GenomeX real-time PCR-based screening test, and three genotypes were identified: homozygous deletion carriers (4 newborns), heterozygous carriers (772 newborns), and wild-type individuals (35,364 newborns). The disease status of all four newborns that screened positive for the homozygous SMN1 deletion was confirmed by alternate methods. Two of the newborns had two copies of SMN2, and two of the newborns had three copies. We determined the incidence of spinal muscular atrophy in Saint Petersburg to be 1 in 9035 and the SMA carrier frequency to be 1 in 47. In conclusion, providing timely information regarding SMN1, confirmation of disease status, and SMN2 copy number as part of the SMA newborn-screening algorithm can significantly improve clinical follow-up, testing of family members, and treatment of patients with SMA.
Collapse
Affiliation(s)
- Anton Kiselev
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Marianna Maretina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Sofia Shtykalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Haya Al-Hilal
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Maslyanyuk
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Mariya Plokhih
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Elena Serebryakova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Marina Frolova
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Natalia Shved
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Nadezhda Krylova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Arina Il’ina
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Svetlana Freund
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Natalia Osinovskaya
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Iskender Sultanov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anna Egorova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Anastasia Lobenskaya
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Alexander Koroteev
- Saint Petersburg State Medical Diagnostic Center (Genetic Medical Center), Tobolskaya Street 5, 353912 Saint Petersburg, Russia; (M.F.); (A.L.); (A.K.)
| | - Irina Sosnina
- Saint Petersburg State Budgetary Healthcare Institution “Consulting and Diagnostic Center for Children”, Aleksa Dundić Street 36/2, 192289 Saint Petersburg, Russia;
| | - Yulia Gorelik
- Children’s City Multidisciplinary Clinical Specialized Center of High Medical Technologies, Avangardnaya Street 14, 198205 Saint Petersburg, Russia;
| | - Olesya Bespalova
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Vladislav Baranov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Igor Kogan
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| | - Andrey Glotov
- Department of Genomic Medicine Named after V.S. Baranov, D.O. Ott Research Institute of Obstetrics, Gynecology and Reproductology, Mendeleevskaya Line 3, 199034 Saint Petersburg, Russia; (M.M.); (S.S.); (H.A.-H.); (N.M.); (M.P.); (E.S.); (N.S.); (N.K.); (A.I.); (S.F.); (I.S.); (A.E.); (O.B.); (I.K.); (A.G.)
| |
Collapse
|
6
|
Bai J, Qu Y, Huang W, Meng W, Zhan J, Wang H, Hou W, Jin Y, Mao A, Song F. A high-fidelity long-read sequencing-based approach enables accurate and effective genetic diagnosis of spinal muscular atrophy. Clin Chim Acta 2024; 553:117743. [PMID: 38158006 DOI: 10.1016/j.cca.2023.117743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/08/2023] [Accepted: 12/21/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND We aimed to develop a high-fidelity long-read sequencing (LRS)-based approach to detect SMN gene variants in one step. It is challenging for conventional step-wise methods to simultaneously detect all kinds of variations between homologous SMN1 and SMN2. METHODS In this study, LRS was developed to analyze copy numbers (CNs), full sequences, and structure of SMN1 and SMN2. The results were compared with those from the step-wise methods in 202 samples from 67 families. RESULTS LRS achieved 100% (202/202) and 99.5% (201/202) accuracy for SMN1 and SMN2 CNs, respectively. It corrected SMN1 CNs from MLPA, which was caused by SNVs/indels that located in probe-binding region. LRS identified 23 SNVs/indels distributing throughout SMN1, including c.22dup and c.884A > T in trans-configuration, and a de novo variant c.41_42delinsC for the first time. LRS also identified a SMN2 variant c.346A > G. Moreover, it successfully determined Alu-mediated 8978-bp deletion encompassing exon 2a-5 and 1415-bp deletion disrupting exon 1, and the exact breakpoints of large deletions. Through haplotype-based pedigree trio analysis, LRS identified SMN1 2 + 0 carriers, and determined the distribution of SMN1 and SMN2 on two chromosomes. CONCLUSIONS LRS represents a more comprehensive and accurate diagnosis approach that is beneficial to early treatment and effective management of SMA.
Collapse
Affiliation(s)
- Jinli Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Yujin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wenchen Huang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Jiahan Zhan
- Berry Genomics Corporation, Beijing 102200, China
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Wenqi Hou
- Berry Genomics Corporation, Beijing 102200, China
| | - Yuwei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing 100020, China.
| |
Collapse
|
7
|
Zhou Y, Jiang Y. Current Advances in Genetic Testing for Spinal Muscular Atrophy. Curr Genomics 2023; 24:273-286. [PMID: 38235355 PMCID: PMC10790334 DOI: 10.2174/0113892029273388231023072050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/22/2023] [Accepted: 10/02/2023] [Indexed: 01/19/2024] Open
Abstract
Spinal muscular atrophy (SMA) is one of the most common genetic disorders worldwide, and genetic testing plays a key role in its diagnosis and prevention. The last decade has seen a continuous flow of new methods for SMA genetic testing that, along with traditional approaches, have affected clinical practice patterns to some degree. Targeting different application scenarios and selecting the appropriate technique for genetic testing have become priorities for optimizing the clinical pathway for SMA. In this review, we summarize the latest technological innovations in genetic testing for SMA, including MassArray®, digital PCR (dPCR), next-generation sequencing (NGS), and third-generation sequencing (TGS). Implementation recommendations for rationally choosing different technical strategies in the tertiary prevention of SMA are also explored.
Collapse
Affiliation(s)
- Yulin Zhou
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| | - Yu Jiang
- United Diagnostic and Research Center for Clinical Genetics, Women and Children’s Hospital, School of Medicine & School of Public Health, Xiamen University, Xiamen, Fujian 361003, P.R. China
- Biobank, Women and Children’s Hospital, School of Medicine, Xiamen University, Xiamen, Fujian 361003, P.R. China
| |
Collapse
|
8
|
Yu SY, Xi YL, Xu FQ, Zhang J, Liu YS. Application of long read sequencing in rare diseases: The longer, the better? Eur J Med Genet 2023; 66:104871. [PMID: 38832911 DOI: 10.1016/j.ejmg.2023.104871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/11/2023] [Accepted: 10/22/2023] [Indexed: 06/06/2024]
Abstract
Rare diseases encompass a diverse group of genetic disorders that affect a small proportion of the population. Identifying the underlying genetic causes of these conditions presents significant challenges due to their genetic heterogeneity and complexity. Conventional short-read sequencing (SRS) techniques have been widely used in diagnosing and investigating of rare diseases, with limitations due to the nature of short-read lengths. In recent years, long read sequencing (LRS) technologies have emerged as a valuable tool in overcoming these limitations. This minireview provides a concise overview of the applications of LRS in rare disease research and diagnosis, including the identification of disease-causing tandem repeat expansions, structural variations, and comprehensive analysis of pathogenic variants with LRS.
Collapse
Affiliation(s)
- Si-Yan Yu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; The First School of Clinical Medicine, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yu-Lin Xi
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Fu-Qiang Xu
- Department of Gynecology, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Jian Zhang
- Department of Medical Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China.
| | - Yan-Shan Liu
- Department of Pediatric Laboratory, Affiliated Children's Hospital of Jiangnan University (Wuxi Children's Hospital), Wuxi, Jiangsu, China; Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
| |
Collapse
|
9
|
Liu Y, Li D, Yu D, Liang Q, Chen G, Li F, Gao L, Li Z, Xie T, Wu L, Mao A, Wu L, Liang D. Comprehensive Analysis of Hemophilia A (CAHEA): Towards Full Characterization of the F8 Gene Variants by Long-Read Sequencing. Thromb Haemost 2023; 123:1151-1164. [PMID: 37285902 PMCID: PMC10686748 DOI: 10.1055/a-2107-0702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/15/2023] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hemophilia A (HA) is the most frequently occurring X-linked bleeding disorder caused by heterogeneous variants in the F8 gene, one of the largest genes known. Conventional molecular analysis of F8 requires a combination of assays, usually including long-range polymerase chain reaction (LR-PCR) or inverse-PCR for inversions, Sanger sequencing or next-generation sequencing for single-nucleotide variants (SNVs) and indels, and multiplex ligation-dependent probe amplification for large deletions or duplications. MATERIALS AND METHODS This study aimed to develop a LR-PCR and long-read sequencing-based assay termed comprehensive analysis of hemophilia A (CAHEA) for full characterization of F8 variants. The performance of CAHEA was evaluated in 272 samples from 131 HA pedigrees with a wide spectrum of F8 variants by comparing to conventional molecular assays. RESULTS CAHEA identified F8 variants in all the 131 pedigrees, including 35 intron 22-related gene rearrangements, 3 intron 1 inversion (Inv1), 85 SNVs and indels, 1 large insertion, and 7 large deletions. The accuracy of CAHEA was also confirmed in another set of 14 HA pedigrees. Compared with the conventional methods combined altogether, CAHEA assay demonstrated 100% sensitivity and specificity for identifying various types of F8 variants and had the advantages of directly determining the break regions/points of large inversions, insertions, and deletions, which enabled analyzing the mechanisms of recombination at the junction sites and pathogenicity of the variants. CONCLUSION CAHEA represents a comprehensive assay toward full characterization of F8 variants including intron 22 and intron 1 inversions, SNVs/indels, and large insertions and deletions, greatly improving the genetic screening and diagnosis for HA.
Collapse
Affiliation(s)
- Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Dongyi Yu
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Guilan Chen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, Guangdong, China
| | - Lu Gao
- Center for Medical Genetics and Prenatal Diagnosis, Shandong Provincial Maternal and Child Health Care Hospital, Shandong Medicine and Health Key Laboratory of Birth Defect Prevention and Genetic Medicine, Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Jinan, Shandong, China
| | - Zhuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | | | - Le Wu
- Berry Genomics Corporation, Beijing, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Lingqian Wu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Desheng Liang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| |
Collapse
|
10
|
Li S, Han X, Zhang L, Xu Y, Chang C, Gao L, Zhan J, Hua R, Mao A, Wang Y. An Effective and Universal Long-Read Sequencing-Based Approach for SMN1 2 + 0 Carrier Screening through Family Trio Analysis. Clin Chem 2023; 69:1295-1306. [PMID: 37932106 DOI: 10.1093/clinchem/hvad152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/28/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Population-wide carrier screening for spinal muscular atrophy (SMA) is recommended by professional organizations to facilitate informed reproductive options. However, genetic screening for SMN1 2 + 0 carriers, accounting for 3%-8% of all SMA carriers, has been challenging due to the large gene size and long distance between the 2 SMN genes. METHODS Here we repurposed a previously developed long-read sequencing-based approach, termed comprehensive analysis of SMA (CASMA), to identify SMN1 2 + 0 carriers through haplotype analysis in family trios (CASMA-trio). Bioinformatics pipelines were developed for accurate haplotype analysis and SMN1 2 + 0 deduction. Seventy-nine subjects from 24 families composed of, at the minimum, 3 were enrolled, and CASMA-trio was employed to determine whether an index subject with 2 SMN1 copies was a 2 + 0 carrier in these families. For the proof-of-principle, SMN2 2 + 0 was also analyzed. RESULTS Among the 16 subjects with 2 SMN1 copies, CASMA-trio identified 5 subjects from 4 families as SMN1 2 + 0 carriers, which was consistent with pedigree analysis involving an affected proband. CASMA-trio also identified SMN2 2 + 0 in six out of 43 subjects with 2 SMN2 copies. Additionally, CASMA-trio successfully determined the distribution pattern of SMN1 and SMN2 genes on 2 alleles in all 79 subjects. CONCLUSIONS CASMA-trio represents an effective and universal approach for SMN1 2 + 0 carriers screening, as it does not reply on the presence of an affected proband, certain single-nucleotide polymorphisms, ethnicity-specific haplotypes, or complicated single-nucleotide polymorphism analysis across 3 generations. Incorporating CASMA-trio into existing SMA carrier screening programs will greatly reduce residual risk ratio.
Collapse
Affiliation(s)
- Shuyuan Li
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Xu Han
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Liang Zhang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Yan Xu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Chunxin Chang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Li Gao
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Jiahan Zhan
- Berry Genomics Corporation, Beijing 102200, China
| | - Renyi Hua
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China
| | - Yanlin Wang
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai 200030, China
- Institute of Birth Defects and Rare Diseases, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China
| |
Collapse
|
11
|
Hou F, Mao A, Shan S, Li Y, Meng W, Zhan J, Nie W, Jin H. Evaluating the clinical utility of a long-read sequencing-based approach in genetic testing of fragile-X syndrome. Clin Chim Acta 2023; 551:117614. [PMID: 38375623 DOI: 10.1016/j.cca.2023.117614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 02/21/2024]
Abstract
BACKGROUND Fragile X syndrome (FXS) arises from the FMR1 CGG expansion. Comprehensive genetic testing for FMR1 CGG expansions, AGG interruptions, and microdeletions is essential to provide genetic counseling for females carrying premutation alleles. However, conventional PCR-based FMR1 assays mainly focus on CGG repeats, and could detect AGG interruption only in males. METHODS The clinical utility of a long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was evaluated in 238 high-risk samples by comparing to conventional PCR assays. RESULTS PCR assays identified five premuation and three full mutation categories alleles in all the samples, and CAFXS successfully called all the FMR1 CGG expansion. CAFXS identified 24-bp microdeletions upstream to the trinucleotide region with 30 CGG repeats, which was miscalled by the length-based PCR methods. CAFXS also identified a 187-bp deletion in about 1/7 of the sequencing reads in a male patient with mosaic full mutation alleles. CAFXS allowed for precise constructing the FMR1 CGG repeat and AGG interruption pattern in all the samples, and identified a novel and alternative CGA interruption in one normal female sample. CONCLUSIONS CAFXS represents a more comprehensive and accurate approach for FXS genetic testing that potentially enables more informed genetic counseling compared to PCR-based methods.
Collapse
Affiliation(s)
- Fei Hou
- Department of Prenatal Diagnosis, Jinan Maternal and Child Health Hospital, Jinan 250001, Shandong Province, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing 102200, China
| | - Shan Shan
- Department of Prenatal Diagnosis, Jinan Maternal and Child Health Hospital, Jinan 250001, Shandong Province, China
| | - Yan Li
- Department of Prenatal Diagnosis, Jinan Maternal and Child Health Hospital, Jinan 250001, Shandong Province, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing 102200, China
| | - Jiahan Zhan
- Berry Genomics Corporation, Beijing 102200, China
| | - Wenying Nie
- Department of Prenatal Diagnosis, Jinan Maternal and Child Health Hospital, Jinan 250001, Shandong Province, China
| | - Hua Jin
- Department of Prenatal Diagnosis, Jinan Maternal and Child Health Hospital, Jinan 250001, Shandong Province, China.
| |
Collapse
|
12
|
Ling X, Wang C, Li L, Pan L, Huang C, Zhang C, Huang Y, Qiu Y, Lin F, Huang Y. Third-generation sequencing for genetic disease. Clin Chim Acta 2023; 551:117624. [PMID: 37923104 DOI: 10.1016/j.cca.2023.117624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 11/07/2023]
Abstract
Third-generation sequencing (TGS) has led to a brave new revolution in detecting genetic diseases over the last few years. TGS has been rapidly developed for genetic disease applications owing to its significant advantages such as long read length, rapid detection, and precise detection of complex and rare structural variants. This approach greatly improves the efficiency of disease diagnosis and complements the shortcomings of short-read sequencing. In this paper, we first briefly introduce the working mechanism of one of the most important representatives of TGS, single-molecule real-time (SMRT) sequencing by Pacific Bioscience (PacBio), followed by a review and comparison of the advantages and disadvantages of different sequencing technologies. Finally, we focused on the progress of SMRT sequencing applications in genetic disease detection. Future perspectives on the applications of TGS in other fields were also presented. With the continuous innovation of the SMRT technologies and the expansion of their fields of application, SMRT sequencing has broad clinical application prospects in genetic diseases detection, and is expected to become an important tool for the molecular diagnosis of other diseases.
Collapse
Affiliation(s)
- Xiaoting Ling
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chenghan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Linlin Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Liqiu Pan
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Chaoyu Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Caixia Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yunhua Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China
| | - Yuling Qiu
- NHC Key Laboratory of Thalassemia Medicine, Guangxi Medical University, Nanning 530021, China; Guangxi Key Laboratory of Thalassemia Research, Guangxi Medical University, Nanning 530021, China
| | - Faquan Lin
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
| | - Yifang Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Guangxi Medical University, Nanning 530021, China.
| |
Collapse
|
13
|
Davidson JE, Russell JS, Martinez NN, Mowat DR, Jones KJ, Kirk EP, Kariyawasam D, Farrar M, D’Silva A. The Carrier Frequency of Two SMN1 Genes in Parents of Symptomatic Children with SMA and the Significance of SMN1 Exon 8 in Carriers. Genes (Basel) 2023; 14:1403. [PMID: 37510307 PMCID: PMC10379112 DOI: 10.3390/genes14071403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/03/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND Current carrier screening methods do not identify a proportion of carriers that may have children affected by spinal muscular atrophy (SMA). Additional genetic data is essential to inform accurate risk assessment and genetic counselling of SMA carriers. This study aims to quantify the various genotypes among parents of children with SMA. METHOD A retrospective cohort study was undertaken at Sydney Children's Hospital Network, the major SMA referral centre for New South Wales, Australia. Participants included children with genetically confirmed SMA born between 2005 and 2021. Data was collected on parent genotype inclusive of copy number of SMN1 exons 7 and 8. The number of SMN2 exon 7 copies were recorded for the affected children. Descriptive statistics were used to determine the proportion of carriers of 2+0 genotype classified as silent carriers. Chi-square test was used to correlate the association between parents with a heterozygous SMN1 exon 7 deletion and two copies of exon 8 and ≥3 SMN2 copy number in the proband. RESULTS SMA carrier testing was performed in 118/154 (76.6%) parents, incorporating 59 probands with homozygous SMN1 deletions and one proband with compound heterozygote pathogenic variants. Among parents with a child with SMA, 7.6% had two copies of SMN1 exon 7. When only probands with a homozygous SMN1 exon 7 deletion were included, 6.9% of parents had two copies of SMN1 exon 7. An association was observed between heterozygous deletion of SMN1 exon 7 with two copies of exon 8 in a parent and ≥3 SMN2 copy number in the affected proband (p = 0.07). CONCLUSIONS This study confirmed a small but substantial proportion of silent carriers not identified by conventional screening within an Australian context. Accordingly, the effectiveness of carrier screening for SMA is linked with genetic counselling to enable health literacy regarding high and low risk results and is complemented by new-born screening and maintaining clinical awareness for SMA. Gene conversion events may underpin the associations between parent carrier status and proband SMN2 copy number.
Collapse
Affiliation(s)
- Joanne E Davidson
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
| | - Jacqueline S Russell
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - Noelia Nunez Martinez
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - David R Mowat
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
| | - Kristi J Jones
- Department of Clinical Genetics, The Children’s Hospital at Westmead, and Discipline of Paediatrics and Child Health, University of Sydney, Sydney, NSW 2006, Australia
| | - Edwin P Kirk
- Centre for Clinical Genetics, Sydney Children’s Hospital, Randwick, Sydney, NSW 2031, Australia; (J.S.R.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Didu Kariyawasam
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Michelle Farrar
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| | - Arlene D’Silva
- Department of Neurology, Sydney Children’s Hospitals Network, Sydney, NSW 2031, Australia; (J.E.D.)
- Discipline of Paediatrics and Child Health, School of Clinical Medicine, University of New South Wales Sydney, Sydney, NSW 2052, Australia
| |
Collapse
|
14
|
Chen X, Harting J, Farrow E, Thiffault I, Kasperaviciute D, Hoischen A, Gilissen C, Pastinen T, Eberle MA. Comprehensive SMN1 and SMN2 profiling for spinal muscular atrophy analysis using long-read PacBio HiFi sequencing. Am J Hum Genet 2023; 110:240-250. [PMID: 36669496 PMCID: PMC9943720 DOI: 10.1016/j.ajhg.2023.01.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/21/2023] Open
Abstract
Spinal muscular atrophy, a leading cause of early infant death, is caused by bi-allelic mutations of SMN1. Sequence analysis of SMN1 is challenging due to high sequence similarity with its paralog SMN2. Both genes have variable copy numbers across populations. Furthermore, without pedigree information, it is currently not possible to identify silent carriers (2+0) with two copies of SMN1 on one chromosome and zero copies on the other. We developed Paraphase, an informatics method that identifies full-length SMN1 and SMN2 haplotypes, determines the gene copy numbers, and calls phased variants using long-read PacBio HiFi data. The SMN1 and SMN2 copy-number calls by Paraphase are highly concordant with orthogonal methods (99.2% for SMN1 and 100% for SMN2). We applied Paraphase to 438 samples across 5 ethnic populations to conduct a population-wide haplotype analysis of these highly homologous genes. We identified major SMN1 and SMN2 haplogroups and characterized their co-segregation through pedigree-based analyses. We identified two SMN1 haplotypes that form a common two-copy SMN1 allele in African populations. Testing positive for these two haplotypes in an individual with two copies of SMN1 gives a silent carrier risk of 88.5%, which is significantly higher than the currently used marker (1.7%-3.0%). Extending beyond simple copy-number testing, Paraphase can detect pathogenic variants and enable potential haplotype-based screening of silent carriers through statistical phasing of haplotypes into alleles. Future analysis of larger population data will allow identification of more diverse haplotypes and genetic markers for silent carriers.
Collapse
Affiliation(s)
| | | | - Emily Farrow
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pediatrics, Children’s Mercy Kansas City, Kansas City, MO, USA
| | - Isabelle Thiffault
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA,Department of Pathology and Laboratory Medicine, Children’s Mercy Kansas City, Kansas City, MO, USA
| | | | | | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Expertise Center for Immunodeficiency and Autoinflammation and Radboud Center for Infectious Disease (RCI), Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Tomi Pastinen
- Genomic Medicine Center, Children’s Mercy Kansas City, Kansas City, MO, USA,UMKC School of Medicine, University of Missouri Kansas City, Kansas City, MO, USA
| | | |
Collapse
|
15
|
Liang Q, Liu Y, Liu Y, Duan R, Meng W, Zhan J, Xia J, Mao A, Liang D, Wu L. Comprehensive Analysis of Fragile X Syndrome: Full Characterization of the FMR1 Locus by Long-Read Sequencing. Clin Chem 2022; 68:1529-1540. [PMID: 36171182 DOI: 10.1093/clinchem/hvac154] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/21/2022] [Indexed: 11/14/2022]
Abstract
BACKGROUND Fragile X syndrome (FXS) is the most frequent cause of inherited X-linked intellectual disability. Conventional FXS genetic testing methods mainly focus on FMR1 CGG expansions and fail to identify AGG interruptions, rare intragenic variants, and large gene deletions. METHODS A long-range PCR and long-read sequencing-based assay termed comprehensive analysis of FXS (CAFXS) was developed and evaluated in Coriell and clinical samples by comparing to Southern blot analysis and triplet repeat-primed PCR (TP-PCR). RESULTS CAFXS accurately detected the number of CGG repeats in the range of 93 to at least 940 with mass fraction of 0.5% to 1% in the background of normal alleles, which was 2-4-fold analytically more sensitive than TP-PCR. All categories of mutations detected by control methods, including full mutations in 30 samples, were identified by CAFXS for all 62 clinical samples. CAFXS accurately determined AGG interruptions in all 133 alleles identified, even in mosaic alleles. CAFXS successfully identified 2 rare intragenic variants including the c.879A > C variant in exon 9 and a 697-bp microdeletion flanking upstream of CGG repeats, which disrupted primer annealing in TP-PCR assay. In addition, CAFXS directly determined the breakpoints of a 237.1-kb deletion and a 774.0-kb deletion encompassing the entire FMR1 gene in 2 samples. CONCLUSIONS Long-read sequencing-based CAFXS represents a comprehensive assay for identifying FMR1 CGG expansions, AGG interruptions, rare intragenic variants, and large gene deletions, which greatly improves the genetic screening and diagnosis for FXS.
Collapse
Affiliation(s)
- Qiaowei Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Yingdi Liu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yaning Liu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Ranhui Duan
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Wanli Meng
- Berry Genomics Corporation, Beijing, China
| | | | - Jiahui Xia
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China
| | - Aiping Mao
- Berry Genomics Corporation, Beijing, China
| | - Desheng Liang
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lingqian Wu
- Department of Medical Genetics, Hunan Jiahui Genetics Hospital, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| |
Collapse
|