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Targeted next-generation sequencing identifies eighteen novel mutations expanding the molecular and clinical spectrum of PKLR gene disorders in the Indian population

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Abstract

Pyruvate kinase deficiency (PKD) is an autosomal recessive condition, caused due to homozygous or compound heterozygous mutation in the PKLR gene resulting in non-spherocytic hereditary hemolytic anemia. Clinical manifestations in PKD patients vary from moderate to severe lifelong hemolytic anemia either requiring neonatal exchange transfusion or blood transfusion support. Measuring PK enzyme activity is the gold standard approach for diagnosis but residual activity must be related to the increased reticulocyte count. The confirmatory diagnosis is provided by PKLR gene sequencing by conventional as well as targeted next-generation sequencing involving genes associated with enzymopathies, membranopathies, hemoglobinopathies, and bone marrow failure disorders. In this study, we report the mutational landscape of 45 unrelated PK deficiency cases from India. The genetic sequencing of PKLR revealed 40 variants comprising 34 Missense Mutations (MM), 2 Nonsense Mutations (NM), 1 Splice site, 1 Intronic, 1 Insertion, and 1 Large Base Deletion. The 17 novel variants identified in this study are A115E, R116P, A423G, K313I, E315G, E318K, L327P, M377L, A423E, R449G, H507Q, E538K, G563S, c.507 + 1 G > C, c.801_802 ins A (p.Asp268ArgfsTer48), IVS9dsA-T + 3, and one large base deletion. In combination with previous reports on PK deficiency, we suggest c.880G > A, c.943G > A, c.994G > A, c.1456C > T, c.1529G > A are the most frequently observed mutations in India. This study expands the phenotypic and molecular spectrum of PKLR gene disorders and also emphasizes the importance of combining both targeted next-generation sequencing with bioinformatics analysis and detailed clinical evaluation to elaborate a more accurate diagnosis and correct diagnosis for transfusion dependant hemolytic anemia in a cohort of the Indian population.

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Whole data are summarized in Tables 1 and 2. For Figs. 1, 2 and 3, any specific data related to the methodology are available on request from the authors.

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Acknowledgements

We would like to thank patients and family members for their cooperation and participation in this study. This study was performed with the support of the Indian Council of Medical Research New Delhi for ICMR SRF to Ms. Rashmi Dongerdiye and the Department of Biotechnology (DBT) New Delhi for financial support.

Funding

This study was performed with the financial support of the Indian Council of Medical Research New Delhi and the Department of Biotechnology New Delhi (DBT Project No. BT/PR20782/MED/12/737/2016) also received financial support from ICMR, New Delhi for providing senior research fellowship to Ms. Rashmi Dongerdiye.

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Authors and Affiliations

  1. Department of Haematogenetics, ICMR-National Institute of Immunohematology, 13th Floor, NMS Building, King Edward Memorial (KEM) Hospital Campus, Parel, 400012, Mumbai, India

    Rashmi Dongerdiye, Meghana Bokde, Tejashree Anil More, Arati Saptarshi, Rati Devendra, Ashish Chiddarwar, Prashant Warang & Prabhakar Kedar

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  1. Rashmi Dongerdiye
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  2. Meghana Bokde
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  8. Prabhakar Kedar
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Contributions

Prabhakar Kedar: conceptualization, data curation, funding acquisition, investigation, project administration, methodology, supervision, and writing—review and editing. Rashmi Dongerdiye: conceptualization, data curation, formal analysis, methodology, and writing—original draft. Bioinformatics software analysis.

Arati Saptarshi, Tejashree More, Meghana Bokade, Rati Devendra, Ashish Chiddarwar, and Prashant Warang: data curation, laboratory analysis, methodology.

Corresponding author

Correspondence to Prabhakar Kedar.

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Ethical approval

The study has been carried out in agreement with the research rules of our institutional ethical committee on human testing. This study has been approved by the National Institute of Immunohematology Ethical committee and as per protocol, written informed consent was obtained from all the patients or their parents. All the authors of this manuscript do not have any conflict of interest.

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Dongerdiye, R., Bokde, M., More, T.A. et al. Targeted next-generation sequencing identifies eighteen novel mutations expanding the molecular and clinical spectrum of PKLR gene disorders in the Indian population. Ann Hematol 102, 1029–1036 (2023). https://doi.org/10.1007/s00277-023-05152-2

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