scholarly journals Preimplantation genetic testing for a family with usher syndrome through targeted sequencing and haplotype analysis

2019 ◽  
Vol 12 (1) ◽  
Author(s):  
Haining Luo ◽  
Chao Chen ◽  
Yun Yang ◽  
Yinfeng Zhang ◽  
Yuan Yuan ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Rare Variant ◽  
Genomic Dna ◽  
Haplotype Analysis ◽  
Multiple Displacement Amplification ◽  
Usher Syndrome ◽  
Nucleotide Polymorphisms ◽  
Preimplantation Genetic Testing ◽  
Targeted Capture ◽  
Capture Sequencing

Abstract Background Preimplantation genetic testing for monogenic defects (PGT-M) has been available in clinical practice. This study aimed to validate the applicability of targeted capture sequencing in developing personalized PGT-M assay. Methods One couple at risk of transmitting Usher Syndrome to their offspring was recruited to this study. Customized capture probe targeted at USH2A gene and 350 kb flanking region were designed for PGT-M. Eleven blastocysts were biopsied and amplified by using multiple displacement amplification (MDA) and capture sequencing. A hidden Markov model (HMM) assisted haplotype analysis was performed to deduce embryo’s genotype by using single nucleotide polymorphisms (SNPs) identified in each sample. The embryo without paternal rare variant was implanted and validated by conventional prenatal or postnatal diagnostic means. Results Four embryos were diagnosed as free of father’s rare variant, two were transferred and one achieved a successful pregnancy. The fetal genotype was confirmed by Sanger sequencing of fetal genomic DNA obtained by amniocentesis. The PGT-M and prenatal diagnosis results were further confirmed by the molecular diagnosis of the baby’s genomic DNA sample. The auditory test showed that the hearing was normal. Conclusions Targeted capture sequencing is an effective and convenient strategy to develop customized PGT-M assay.

scholarly journals Pre-implantation genetic diagnosis for a family with Usher syndrome through targeted sequencing and haplotype analysis

2018 ◽  
Author(s):  
Haining Luo ◽  
Chao Chen ◽  
Yun Yang ◽  
Yuan Yuan ◽  
Wanyang Wang ◽  
...  
Keyword(s):  
Molecular Diagnosis ◽  
Genomic Dna ◽  
Haplotype Analysis ◽  
Massively Parallel Sequencing ◽  
Multiple Displacement Amplification ◽  
Usher Syndrome ◽  
Genetic Diagnosis ◽  
Massively Parallel ◽  
Parallel Sequencing ◽  
Targeted Capture

AbstractObjectiveOur objective was to investigate the applicability of targeted capture massively parallel sequencing in developing personalized pre-implantation genetic diagnosis (PGD) assay.MethodsOne couple at risk of transmitting Usher Syndrome to their offspring was recruited to this study. The genomics DNA (gDNA) was extracted from the peripheral blood and underwent in vitro fertilization (IVF)-PGD. Prenatal molecular diagnosis was performed in the 20th week of gestation and the chromosomal anomaly was analyzed.ResultsCustomized capture probe targeted at USH2A gene and 350kb flanking region were designed for PGD. Eleven blastocysts were biopsied and amplified by using multiple displacement amplification (MDA) and capture sequencing. A HMM-based haplotype analysis was performed to deduce embryo’s genotype by using SNPs identified in each sample. Four embryos were diagnosed as free of father’s rare mutation, two were transferred and one achieved a successful pregnancy. The fetal genotype was confirmed by Sanger sequencing of fetal genomic DNA obtained by amniocentesis. The PGD and prenatal diagnosis results were further confirmed by the molecular diagnosis of the baby’s genomic DNA sample. The auditory test showed that the hearing was normal.ConclusionTargeted capture massively parallel sequencing (MPS) is an effective and convenient strategy to develop customized PGD assay.Key pointsGenetic counseling session was conducted with a family having Usher patient who was molecularly diagnosed, and a healthy baby was born with the help of successful PGD assay. This is of vast importance in management plans since it is the first report of PGD in Usher syndrome based on targeted capture MPS.

scholarly journals Haplotyping by linked-read sequencing (HLRS) of the genetic disease carriers for preimplantation genetic testing without a proband or relatives

2020 ◽  
Author(s):  
Qing Li ◽  
Yan Mao ◽  
Shaoying Li ◽  
Hongzi Du ◽  
Wenzhi He ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genetic Disease ◽  
De Novo ◽  
Monogenic Disease ◽  
Nucleotide Polymorphisms ◽  
De Novo Mutations ◽  
Preimplantation Genetic Testing ◽  
Linkage Analyses ◽  
Alpha Thalassemia ◽  
Polar Bodies

Abstract Background: In order to mitigate the risk of allele dropout (ADO) and ensure the accuracy of preimplantation genetic testing for monogenic disease (PGT-M), it is necessary to construct parental haplotypes.. Typically, haplotype resolution is obtained by genotyping multiple polymorphic markers in both parents and a proband or a relative. Sometimes, single sperm typing, or tests on the polar bodies may also be useful. Nevertheless, this process is time-consuming. At present, there was no simple linkage analysis strategy for patients without affected relatives.Method: To solve this problem, we established a haplotyping by linked-read sequencing (HLRS) method without the requirement for additional relatives. First, the haplotype of the genetic disease carriers in the family was constructed by linked-read sequencing, and then the informative single nucleotide polymorphisms (SNPs) in upstream and downstream mutation region were selected to construct the embryo haplotype and to determine whether the embryo was carrying the mutation. Two families were selected to validate this method; one with alpha thalassemia and the other with NDP gene disorder.Results: The haplotyping by linked-read sequencing (HLRS) method was successfully applied to construct parental haplotypes without recruiting additional family members; the method was also validated for PGT-M. The mutation carriers in these families were sequenced by linked-read sequencing, and their haplotypes were successfully phased. Adjacent SNPs of the mutation gene were identified. The informative SNPs were chosen for linkage analyses to identify the carrier embryos. For the alpha thalassemia family, a normal blastocyst was transferred to the uterus and the accuracy of PGT-M was confirmed by amniocentesis at 16 weeks of gestation. Conclusions: Our results suggest that HLRS can be applied for PGT-M of monogenic disorders or de novo mutations where the mutations haplotype cannot be determined due to absence of affected relatives. Keywords: Preimplantation Genetic Testing for monogenic disease, Linked-read sequencing, Linkage analyses, Haplotype

scholarly journals Repeat genetic testing with targeted capture sequencing in primary arrhythmia syndrome and cardiomyopathy

2017 ◽  
Vol 25 (12) ◽  
pp. 1313-1323 ◽  
Author(s):  
Tomas Robyns ◽  
Cuno Kuiperi ◽  
Jeroen Breckpot ◽  
Koenraad Devriendt ◽  
Erika Souche ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Targeted Capture ◽  
Capture Sequencing

Preimplantation genetic testing using haplotype-based single nucleotide polymorphisms analysis

2021 ◽  
Vol 5_2021 ◽  
pp. 100-107
Author(s):  
Ekimov A.N. Ekimov ◽  
Karetnikova N.A. Karetnikova ◽  
Shubina E.S. Shubina ◽  
Gol'tsov A.Yu. Gol'tsov ◽  
Kuznetsova M.V. Kuznetsova ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Preimplantation Genetic Testing ◽  
Single Nucleotide

scholarly journals Preimplantation genetic testing for a chr14q32 microdeletion in a family with Kagami-Ogata syndrome and Temple syndrome

2021 ◽  
pp. jmedgenet-2020-107433
Author(s):  
Joan Sabria-Back ◽  
Ana Monteagudo-Sánchez ◽  
Marta Sánchez-Delgado ◽  
Anne C Ferguson-Smith ◽  
Olga Gómez ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Multiple Displacement Amplification ◽  
In Vitro Fertilisation ◽  
Risk Haplotype ◽  
Single Family ◽  
Preimplantation Genetic Testing ◽  
Genome Wide ◽  
Intracytoplasmatic Sperm Injection ◽  
Temple Syndrome

IntroductionKagami-Ogata syndrome (KOS14) and Temple syndrome (TS14) are two disorders associated with reciprocal alterations within the chr14q32 imprinted domain. Here, we present a work-up strategy for preimplantation genetic testing (PGT) to avoid the transmission of a causative micro-deletion.MethodsWe analysed DNA from the KOS14 index case and parents using methylation-sensitive ligation-mediated probe amplification and methylation pyrosequencing. The extent of the deletion was mapped using SNP arrays. PGT was performed in trophectoderm samples in order to identify unaffected embryos. Samples were amplified using multiple displacement amplification, followed by genome-wide SNP genotyping to determine the at-risk haplotype and next-generation sequencing to determine aneuploidies.ResultsA fully methylated pattern at the normally paternally methylated IG-DMR and MEG3 DMR in the KOS14 proband, accompanied by an unmethylated profile in the TS14 mother was consistent with maternal and paternal transmission of a deletion, respectively. Further analysis revealed a 108 kb deletion in both cases. The inheritance of the deletion on different parental alleles was consistent with the opposing phenotypes. In vitro fertilisation with intracytoplasmatic sperm injection and PGT were used to screen for deletion status and to transfer an unaffected embryo in this couple. A single euploid-unaffected embryo was identified resulting in a healthy baby born.DiscussionWe identify a microdeletion responsible for multigeneration KOS14 and TS14 within a single family where carriers have a 50% risk of transmitting the deletion to their offspring. We show that PGT can successfully be offered to couples with IDs caused by genetic anomalies.

scholarly journals Identification of theTMEM232 gene associated with atopic dermatitis through targeted capture sequencing

2021 ◽  
Author(s):  
Jie Zheng ◽  
Yuan-yuan Wu ◽  
Wen-liang Fang ◽  
Xin-ying Cai ◽  
Zeng-yun-ou Zhang ◽  
...  
Keyword(s):  
Atopic Dermatitis ◽  
Skin Disorder ◽  
Haplotype Analysis ◽  
Susceptibility Gene ◽  
Enrichment Analysis ◽  
Sequencing Analysis ◽  
Loss Of Function ◽  
Gene Level ◽  
Targeted Capture ◽  
Capture Sequencing

AbstractBACKGROUNDAtopic dermatitis (AD) is a common and complex skin disorder, and the 5q22.1 region had been reported to be associated with AD.OBJECTIVETo identify the susceptibility gene for AD in the 5q22.1 region by haplotype and targeted capture sequencing.METHODSThe haplotypes were reconstructed with our previously genotyping data of four SNPs and six deletions from 3055 Chinese Hans AD patients and 4346 controls. The targeted capture sequencing spanning 5q22.1 region was performed in the selected samples. The gene level enrichment analysis was done using loss of function variants.RESULTSA total of 60 haplotypes were found, and the H15 haplotype had the strongest association with AD (P = 2.72×10 −10, OR = 0.14, 95%CI = 0.07-0.28). However, No co-segregation mutation sites were found in the sequencing analysis within the 16 selected samples, while the enrichment analysis indicated that TMEM232 was significantly associated with AD (P = 7.33×10 -5, OR = 0.33, 95% CI = 0.19-0.58).CONCLUSIONSThis study confirms previous findings that the TMEM232 gene is associated with AD by haplotype analysis and targeted capture sequencing.

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