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Maqbool, Khurram
Publications (2 of 2) Show all publications
Shebanits, K., Günther, T., Johansson, A. C. V., Maqbool, K., Feuk, L., Jakobsson, M. & Larhammar, D. (2019). Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.. BMC Biotechnology, 19, Article ID 31.
Open this publication in new window or tab >>Copy number determination of the gene for the human pancreatic polypeptide receptor NPY4R using read depth analysis and droplet digital PCR.
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2019 (English)In: BMC Biotechnology, ISSN 1472-6750, E-ISSN 1472-6750, Vol. 19, article id 31Article in journal (Refereed) Published
Abstract [en]

Background: Copy number variation (CNV) plays an important role in human genetic diversity and has been associated with multiple complex disorders. Here we investigate a CNV on chromosome 10q11.22 that spans NPY4R, the gene for the appetite-regulating pancreatic polypeptide receptor Y4. This genomic region has been challenging to map due to multiple repeated elements and its precise organization has not yet been resolved. Previous studies using microarrays were interpreted to show that the most common copy number was 2 per genome.

Results: We have investigated 18 individuals from the 1000 Genomes project using the well-established method of read depth analysis and the new droplet digital PCR (ddPCR) method. We find that the most common copy number for NPY4R is 4. The estimated number of copies ranged from three to seven based on read depth analyses with Control-FREEC and CNVnator, and from four to seven based on ddPCR. We suggest that the difference between our results and those published previously can be explained by methodological differences such as reference gene choice, data normalization and method reliability. Three high-quality archaic human genomes (two Neanderthal and one Denisova) display four copies of the NPY4R gene indicating that a duplication occurred prior to the human-Neanderthal/Denisova split.

Conclusions: We conclude that ddPCR is a sensitive and reliable method for CNV determination, that it can be used for read depth calibration in CNV studies based on already available whole-genome sequencing data, and that further investigation of NPY4R copy number variation and its consequences are necessary due to the role of Y4 receptor in food intake regulation.

National Category
Cell Biology Genetics
Identifiers
urn:nbn:se:uu:diva-356569 (URN)10.1186/s12896-019-0523-9 (DOI)000470281900001 ()31164119 (PubMedID)
Funder
Swedish Research CouncilThe Swedish Brain Foundation
Available from: 2018-08-01 Created: 2018-08-01 Last updated: 2019-06-25Bibliographically approved
Thuresson, A.-C., Zander, C., Zhao, J. J., Halvardson, J., Maqbool, K., Månsson, E., . . . Feuk, L. (2019). Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability [Letter to the editor]. Clinical Genetics, 95(3), 436-439
Open this publication in new window or tab >>Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability
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2019 (English)In: Clinical Genetics, ISSN 0009-9163, E-ISSN 1399-0004, Vol. 95, no 3, p. 436-439Article in journal, Letter (Refereed) Published
National Category
Medical Genetics
Identifiers
urn:nbn:se:uu:diva-326281 (URN)10.1111/cge.13470 (DOI)000458956100013 ()30525197 (PubMedID)
Funder
EU, European Research Council, 282330
Available from: 2017-07-04 Created: 2017-07-04 Last updated: 2019-03-14Bibliographically approved
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