HBB gene mutation spectrum in an Indian cohort of 1530 cases using an in-house targeted next-generation sequencing assay

被引:0
|
作者
Ketki Kelkar
Vijay Ramanan
Siddharth Anand
Purvi Majethia
Shatakshi Ranade
Kunal Patil
Priyanka Gangodkar
Ashwini Bapat
Asawari Pilankar
Vidula Sengaokar
Kavita Khatod
Meenal Agarwal
Nikhil Phadke
机构
[1] GenePath Diagnostics India Private Limited (GenePath Dx),
[2] MVR Welfare Foundation,undefined
[3] Anjali Diagnostic Pathology Laboratory,undefined
[4] Yashoda Hematology Clinic,undefined
[5] I-SHARE Foundation,undefined
[6] Genepath Diagnostics Inc,undefined
来源
关键词
Beta thalassemia; Mutation spectrum; Novel mutations; Next generation sequencing; ARMS PCR; Capillary sequencing;
D O I
暂无
中图分类号
学科分类号
摘要
Beta thalassemia major is a common genetic disorder characterized by the reduced production or absence of beta globin, a product of the haemoglobin subunit beta (HBB) gene. Every year, approximately 10,000–12,000 children with thalassemia major are born in India. Molecular methodologies like ARMS (amplification-refractory mutation system)-PCR (polymerase chain reaction) and capillary sequencing are used to detect HBB gene mutations. It is, however, challenging to achieve comprehensive coverage of the HBB gene by these methods. Next-generation sequencing (NGS) can be used to circumvent these problems. Commercial NGS panels are prohibitively expensive and hence are not routinely implemented in most laboratories. We have developed a cost-effective, highly sensitive and specific, indigenous targeted NGS assay for detecting mutations in the HBB gene. Using this custom NGS assay, we processed 1530 samples (3017 alleles), in which we detected a spectrum of 48 pathogenic/likely pathogenic variants (mutations); IVS-I-5 (c.92+5G>C) was the most common mutation detected (allele frequency (AF) 44.55%), followed by the 619-bp deletion (AF 10.74%), c.92+1G>T (AF 6.99%), c.27_28insG (AF 6.23%), c.47G>A (AF 5.77%) and c.126_129delCTTT (AF 4.71%). Additionally, we discovered a novel mutation (c.7delC) that was submitted to the HbVar database (HbVar ID 3193) as a variant of unknown significance (VUS), probably pathogenic. The targeted NGS assay developed during this study was validated using orthogonal methods and showed excellent correlation with currently available molecular methods. Additionally, this targeted NGS assay was used to analyse the mutation spectrum of the largest beta thalassemia cohort from India.
引用
收藏
页码:239 / 248
页数:9
相关论文
共 50 条
  • [1] HBB gene mutation spectrum in an Indian cohort of 1530 cases using an in-house targeted next-generation sequencing assay
    Kelkar, Ketki
    Ramanan, Vijay
    Anand, Siddharth
    Majethia, Purvi
    Ranade, Shatakshi
    Patil, Kunal
    Gangodkar, Priyanka
    Bapat, Ashwini
    Pilankar, Asawari
    Sengaokar, Vidula
    Khatod, Kavita
    Agarwal, Meenal
    Phadke, Nikhil
    [J]. JOURNAL OF HEMATOPATHOLOGY, 2020, 13 (04) : 239 - 248
  • [2] Detection of gene rearrangements using OncoPanel: a targeted next-generation sequencing assay
    Garcia, Elizabeth P.
    Ligon, Azra H.
    Abo, Ryan P.
    Dal Cin, Paola S.
    Weremowicz, Stanislawa
    Shivdasani, Priyanka
    Davineni, Phani K.
    Zepfl, Dimity L.
    Ducar, Matthew D.
    Van Hummelen, Paul
    Jia, Yonghui
    Kuo, Frank C.
    Sholll, Lynette M.
    MacConaill, Laura E.
    Lindeman, Neal I.
    [J]. CANCER RESEARCH, 2015, 75
  • [3] Tumor mutation burden assessment on FFPE samples using a targeted next-generation sequencing assay
    Chaudhary, R.
    Cyanam, D.
    Mittal, V.
    Tom, W.
    Au-Young, J.
    Allen, C.
    Sadis, S.
    Hyland, F.
    [J]. ANNALS OF ONCOLOGY, 2018, 29
  • [4] Germline BRCA Mutation Studies in a Select Indian Cohort Using Next-generation Sequencing (NGS)
    Vyas, J. C.
    Pusalkar, M.
    Kittu, R.
    Limaye, S.
    Gomes, A.
    Tibetwala, R.
    Khairnar, S.
    Vora, S.
    Londhe, N.
    Hastak, M.
    Kulkarni, B.
    Athikari, N.
    Goyle, S.
    Nadkarni, M.
    Kulkarni, Y.
    Shetty, A.
    Shaikh, I.
    [J]. JOURNAL OF MOLECULAR DIAGNOSTICS, 2018, 20 (06): : 900 - 900
  • [5] Somatic Mutation Analysis in Melanoma Using Targeted Next-Generation Sequencing
    Miraflor, A. P.
    de Abreu, F. B.
    Peterson, J. D.
    Ernstoff, M. S.
    Amos, C. I.
    Wells, W. A.
    Tsongalis, G. J.
    Yan, S.
    [J]. JOURNAL OF MOLECULAR DIAGNOSTICS, 2014, 16 (06): : 756 - 756
  • [6] Targeted Next-Generation Sequencing Reveals a Large Novel β-Thalassemia Deletion that Removes the Entire HBB Gene
    Yin, Zhen-Zhen
    Yao, Jian
    Wei, Feng-Xiang
    Chen, Chu-Yan
    Yan, Hong-Mei
    Zhang, Ming
    [J]. HEMOGLOBIN, 2022, 46 (05) : 290 - 295
  • [7] Mutation profile of acute myeloid leukaemia in a Chinese cohort by targeted next-generation sequencing
    Lit, Benny Man Wai
    Guo, Belinda B.
    Malherbe, Jacques A. J.
    Kwong, Yok Lam
    Erber, Wendy N.
    [J]. CANCER REPORTS, 2022, 5 (10)
  • [8] Next-Generation Sequencing in a Cohort of Asian Indian Patients with the Duchenne Muscular Dystrophy Phenotype: Diagnostic Yield and Mutation Spectrum
    Nerakh, Gayatri
    Ranganath, Prajnya
    Murugan, Sakthivel
    [J]. JOURNAL OF PEDIATRIC GENETICS, 2021, 10 (01) : 23 - 28
  • [9] Tumour mutation burden assessment from FFPE research samples using a targeted next-generation sequencing assay
    Chaudhary, R.
    Cyanam, D.
    Mittal, V.
    Tom, W.
    Au-Young, J.
    Allen, C.
    Sadis, S.
    Hyland, F.
    [J]. VIRCHOWS ARCHIV, 2018, 473 : S139 - S139
  • [10] A TARGETED NEXT-GENERATION SEQUENCING GENE PANEL FOR AUTOINFLAMMATION
    Omoyinmi, E.
    Standing, A.
    Keylock, A.
    Rowczenio, D.
    Gomes, S. Melo
    Cullup, T.
    Jenkins, L.
    Gilmour, K.
    Eleftheriou, D.
    Lachmann, H.
    Hawkins, P.
    Klein, N.
    Brogan, P.
    [J]. ANNALS OF THE RHEUMATIC DISEASES, 2016, 75 : 667 - 667