Whole genome and exome sequencing realignment supports the assignment of KCNJ12, KCNJ17, and KCNJ18 paralogous genes in thyrotoxic periodic paralysis locus: functional characterization of two polymorphic Kir2.6 isoforms

Whole genome and exome sequencing realignment supports the assignment of KCNJ12, KCNJ17, and KCNJ18 paralogous genes in thyrotoxic periodic paralysis locus: functional characterization of two polymorphic Kir2.6 isoforms

Author Paninka, Rolf M. Autor UNIFESP Google Scholar
Mazzotti, Diego R. Autor UNIFESP Google Scholar
Kizys, Marina M. L. Autor UNIFESP Google Scholar
Vidi, Angela C. Autor UNIFESP Google Scholar
Rodrigues, Helio Autor UNIFESP Google Scholar
Silva, Silas P. Autor UNIFESP Google Scholar
Kunii, Ilda S. Autor UNIFESP Google Scholar
Furuzawa, Gilberto K. Autor UNIFESP Google Scholar
Arcisio-Miranda, Manoel Autor UNIFESP Google Scholar
Dias-da-Silva, Magnus R. Autor UNIFESP Google Scholar
Abstract Next-generation sequencing (NGS) has enriched the understanding of the human genome. However, homologous or repetitive sequences shared among genes frequently produce dubious alignments and can puzzle NGS mutation analysis, especially for paralogous potassium channels. Potassium inward rectifier (Kir) channels are important to establish the resting membrane potential and regulating the muscle excitability. Mutations in Kir channels cause disorders affecting the heart and skeletal muscle, such as arrhythmia and periodic paralysis. Recently, a susceptibility muscle channelopathy-thyrotoxic periodic paralysis (TPP)-has been related to Kir2.6 channel (KCNJ18 gene). Due to their high nucleotide sequence homology, variants found in the potassium channels Kir2.6 and Kir2.5 have been mistakenly attributable to Kir2.2 polymorphisms or mutations. We aimed at elucidating nucleotide misalignments by performing realignment of whole exome sequencing (WES) and whole genome sequencing (WGS) reads to specific Kir2.2, Kir2.5, and Kir2.6 cDNA sequences using BWA-MEM/GATK pipeline. WES/WGS reads correctly aligned 26.9/43.2, 37.6/31.0, and 35.4/25.8 % to Kir2.2, Kir2.5, and Kir2.6, respectively. Realignment was able to reduce over 94 % of misalignments. No putative mutations of Kir2.6 were identified for the three TPP patients included in the cohort of 36 healthy controls using either WES or WGS. We also distinguished sequences for a single Kir2.2, a single Kir2.5 sequence, and two Kir2.6 isoforms, which haplotypes were named RRAI and QHEV, based on changes at 39, 40, 56, and 249 residues. Electrophysiology records on both Kir2.6_RRAI and _QHEV showed typical rectifying currents. In our study, the reduction of misalignments allowed the elucidation of paralogous gene sequences and two distinct Kir2.6 haplotypes, and pointed the need for checking the frequency of these polymorphisms in other populations with different genetic background.
Keywords Potassium inward rectifier channel
Thyrotoxic periodic paralysis
WES
WGS
Electrophysiology
Kir2.6
xmlui.dri2xhtml.METS-1.0.item-coverage Heidelberg
Language English
Sponsor Sao Paulo State Research Foundation-FAPESP
Grant number FAPESP: 2011/20747-8
FAPESP: 2010/52077-9
Date 2016
Published in Molecular Genetics And Genomics. Heidelberg, v. 291, n. 4, p. 1535-1544, 2016.
ISSN 1617-4615 (Sherpa/Romeo, impact factor)
Publisher Springer Heidelberg
Extent 1535-1544
Origin http://dx.doi.org/10.1007/s00438-016-1185-0
Access rights Closed access
Type Article
Web of Science ID WOS:000378995500003
URI https://repositorio.unifesp.br/handle/11600/57514

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