A novel approach to detecting microduplication in split hand/foot malformation type 3 at the single-cell level: SHFM as a case study.
Karyomapping
Microduplication
Next-generation sequencing
Split hand/foot malformation
Whole-genome amplification
Journal
Orphanet journal of rare diseases
ISSN: 1750-1172
Titre abrégé: Orphanet J Rare Dis
Pays: England
ID NLM: 101266602
Informations de publication
Date de publication:
31 Oct 2024
31 Oct 2024
Historique:
received:
24
05
2024
accepted:
25
09
2024
medline:
1
11
2024
pubmed:
1
11
2024
entrez:
1
11
2024
Statut:
epublish
Résumé
Split hand/foot malformation (SHFM) is a congenital limb deficiency characterized by missing or shortened central digits. Several gene loci have been associated with SHFM. Identifying microduplications at the single-cell level is challenging in clinical practice, and traditional detection methods may lead to misdiagnoses in embryos and pregnant women. In this research, we utilized a low cell count and whole-genome amplification products to employ single nucleotide polymorphism arrays, next-generation sequencing, and third-generation sequencing methods to detect copy number variants of microduplications in a SHFM3 case with limited DNA. Additionally, Karyomapping and combined linkage analysis were conducted to validate the results. This study establishes a new strategy for identifying microduplications or microdeletions at the single-cell level in clinical preimplantation genetic testing, enhancing the efficiency and accuracy of diagnosing microduplication or microdeletion diseases during IVF-PGT and prenatal diagnosis.
Sections du résumé
BACKGROUND
BACKGROUND
Split hand/foot malformation (SHFM) is a congenital limb deficiency characterized by missing or shortened central digits. Several gene loci have been associated with SHFM. Identifying microduplications at the single-cell level is challenging in clinical practice, and traditional detection methods may lead to misdiagnoses in embryos and pregnant women.
RESULTS
RESULTS
In this research, we utilized a low cell count and whole-genome amplification products to employ single nucleotide polymorphism arrays, next-generation sequencing, and third-generation sequencing methods to detect copy number variants of microduplications in a SHFM3 case with limited DNA. Additionally, Karyomapping and combined linkage analysis were conducted to validate the results.
CONCLUSIONS
CONCLUSIONS
This study establishes a new strategy for identifying microduplications or microdeletions at the single-cell level in clinical preimplantation genetic testing, enhancing the efficiency and accuracy of diagnosing microduplication or microdeletion diseases during IVF-PGT and prenatal diagnosis.
Identifiants
pubmed: 39482735
doi: 10.1186/s13023-024-03386-5
pii: 10.1186/s13023-024-03386-5
doi:
Types de publication
Case Reports
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
406Subventions
Organisme : National Key R&D program
ID : 2019YFA0802200
Organisme : Innovative Research Group Project of the National Natural Science Foundation of China
ID : 32170819
Organisme : joint fund for the cultivation of superior displines
ID : 222301420013
Organisme : Henan Province University science and technology innovation team
ID : 24IRTSTHN037
Informations de copyright
© 2024. The Author(s).
Références
Czeizel AE, et al. An epidemiological study of isolated split hand/foot in Hungary, 1975–1984. J Med Genet. 1993;30(7):593–6.
doi: 10.1136/jmg.30.7.593
pubmed: 8411034
pmcid: 1016461
Dai L, et al. Prevalence of congenital split hand/split foot malformation in Chinese population. Sichuan Da Xue Xue Bao Yi Xue Ban. 2010;41(2):320–3.
pubmed: 20506663
Velinov M, et al. A 0.7 Mb de novo duplication at 7q21.3 including the genes DLX5 and DLX6 in a patient with split-hand/split-foot malformation. Am J Med Genet A. 2012;158A(12):3201–6.
doi: 10.1002/ajmg.a.35644
pubmed: 23169702
Sowinska-Seidler A, Socha M, Jamsheer A. Split-hand/foot malformation—molecular cause and implications in genetic counseling. J Appl Genet. 2014;55(1):105–15.
doi: 10.1007/s13353-013-0178-5
pubmed: 24163146
Dai L, et al. Discontinuous microduplications at chromosome 10q24.31 identified in a Chinese family with split hand and foot malformation. BMC Med Genet. 2013;14:45.
doi: 10.1186/1471-2350-14-45
pubmed: 23596994
pmcid: 3637097
Sulik KK, Dehart DB. Retinoic-acid-induced limb malformations resulting from apical ectodermal ridge cell death. Teratology. 1988;37(6):527–37.
doi: 10.1002/tera.1420370602
pubmed: 3165225
Scherer SW, et al. Fine mapping of the autosomal dominant split hand/split foot locus on chromosome 7, band q21.3–q22.1. Am J Hum Genet. 1994;55(1):12–20.
pubmed: 8023840
pmcid: 1918243
Gurrieri F, Everman DB. Clinical, genetic, and molecular aspects of split-hand/foot malformation: an update. Am J Med Genet A. 2013;161A(11):2860–72.
doi: 10.1002/ajmg.a.36239
pubmed: 24115638
Sivasankaran A, et al. Split hand/foot malformation associated with 7q21.3 microdeletion: a case report. Mol Syndromol. 2016;6(6):287–96.
doi: 10.1159/000443708
pubmed: 27022330
pmcid: 4802982
Shamseldin HE, et al. Identification of a novel DLX5 mutation in a family with autosomal recessive split hand and foot malformation. J Med Genet. 2012;49(1):16–20.
doi: 10.1136/jmedgenet-2011-100556
pubmed: 22121204
van Silfhout AT, et al. Split hand/foot malformation due to chromosome 7q aberrations(SHFM1): additional support for functional haploinsufficiency as the causative mechanism. Eur J Hum Genet. 2009;17(11):1432–8.
doi: 10.1038/ejhg.2009.72
pubmed: 19401716
pmcid: 2986677
Faiyaz-Ul-Haque M, et al. Fine mapping of the X-linked split-hand/split-foot malformation (SHFM2) locus to a 5.1-Mb region on Xq26.3 and analysis of candidate genes. Clin Genet. 2005;67(1):93–7.
doi: 10.1111/j.1399-0004.2004.00369.x
pubmed: 15617554
Faiyaz ul Haque M, et al. Mapping of the gene for X-chromosomal split-hand/split-foot anomaly to Xq26-q26.1. Hum Genet. 1993;91(1):17–9.
doi: 10.1007/BF00230215
pubmed: 8454282
Qiu L, et al. Microduplication of BTRC detected in a Chinese family with split hand/foot malformation type 3. Clin Genet. 2022;102(5):451–6.
doi: 10.1111/cge.14204
pubmed: 35908152
Ianakiev P, et al. Split-hand/split-foot malformation is caused by mutations in the p63 gene on 3q27. Am J Hum Genet. 2000;67(1):59–66.
doi: 10.1086/302972
pubmed: 10839977
pmcid: 1287102
Koster MI, et al. p63 is the molecular switch for initiation of an epithelial stratification program. Genes Dev. 2004;18(2):126–31.
doi: 10.1101/gad.1165104
pubmed: 14729569
pmcid: 324418
Boles RG, et al. Deletion of chromosome 2q24-q31 causes characteristic digital anomalies: case report and review. Am J Med Genet. 1995;55(2):155–60.
doi: 10.1002/ajmg.1320550204
pubmed: 7717414
Goodman FR, et al. A 117-kb microdeletion removing HOXD9-HOXD13 and EVX2 causes synpolydactyly. Am J Hum Genet. 2002;70(2):547–55.
doi: 10.1086/338921
pubmed: 11778160
pmcid: 384929
Khan S, et al. A novel homozygous missense mutation in WNT10B in familial split-hand/foot malformation. Clin Genet. 2012;82(1):48–55.
doi: 10.1111/j.1399-0004.2011.01698.x
pubmed: 21554266
Blattner A, Huber AR, Rothlisberger B. Homozygous nonsense mutation in WNT10B and sporadic split-hand/foot malformation (SHFM) with autosomal recessive inheritance. Am J Med Genet A. 2010;152A(8):2053–6.
doi: 10.1002/ajmg.a.33504
pubmed: 20635353
Lezirovitz K, et al. A novel locus for split-hand/foot malformation associated with tibial hemimelia (SHFLD syndrome) maps to chromosome region 17p13.1–17p13.3. Hum Genet. 2008;123(6):625–31.
doi: 10.1007/s00439-008-0515-7
pubmed: 18493797
Volozonoka L, Miskova A, Gailite L. Whole genome amplification in preimplantation genetic testing in the era of massively parallel sequencing. Int J Mol Sci. 2022;23(9):4819.
doi: 10.3390/ijms23094819
pubmed: 35563216
pmcid: 9102663
Xie P, et al. A novel multifunctional haplotyping-based preimplantation genetic testing for different genetic conditions. Hum Reprod. 2022;37(11):2546–59.
doi: 10.1093/humrep/deac190
pubmed: 36066440
Geraedts J, Sermon K. Preimplantation genetic screening 2.0: the theory. Mol Hum Reprod. 2016;22(8):839–44.
doi: 10.1093/molehr/gaw033
pubmed: 27256482
pmcid: 4986416
Xie P, et al. Segmental aneuploidies with 1 Mb resolution in human preimplantation blastocysts. Genet Med. 2022;24(11):2285–95.
doi: 10.1016/j.gim.2022.08.008
pubmed: 36107168
Sabria-Back J, et al. Preimplantation genetic testing for a chr14q32 microdeletion in a family with Kagami-Ogata syndrome and Temple syndrome. J Med Genet. 2022;59(3):253–61.
doi: 10.1136/jmedgenet-2020-107433
pubmed: 33579810
Girirajan S, et al. Phenotypic heterogeneity of genomic disorders and rare copy-number variants. N Engl J Med. 2012;367(14):1321–31.
doi: 10.1056/NEJMoa1200395
pubmed: 22970919
pmcid: 3494411
Yan L, et al. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci U S A. 2015;112(52):15964–9.
doi: 10.1073/pnas.1523297113
pubmed: 26712022
pmcid: 4702982
Richards S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17(5):405–24.
doi: 10.1038/gim.2015.30
pubmed: 25741868
pmcid: 4544753
den Dunnen JT. Sequence variant descriptions: HGVS nomenclature and mutalyzer. Curr Protoc Hum Genet. 2016;90:7–13.
Kearney HM, et al. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 2011;13(7):680–5.
doi: 10.1097/GIM.0b013e3182217a3a
pubmed: 21681106
Brown S. Identity-by-state analysis: a new method for PGT-M. Hum Reprod. 2020;35(3):485–7.
doi: 10.1093/humrep/deaa011
pubmed: 32198500