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Author(s):  
Lin Wang ◽  
Bin He ◽  
Qiujie Jin ◽  
Ruimiao Bai ◽  
Wenwen Yu ◽  
...  

Abstract Objectives Phenylketonuria (PKU) is an inherited autosomal recessive disorder of phenylalanine metabolism. It is mainly caused by a deficiency in phenylalanine hydroxylase (PAH) and frequently diagnosed with Sanger sequencing. To some extent, allelic dropout can explain the inconsistency in genotype and phenotype. Methods Three families were evaluated through DNA sequence analysis, multiplex ligation-dependent probe amplification (MLPA) and prenatal diagnosis technologies. The possibility of inconsistency in phenotype and genotype with c.331C>T variant was analysed. Results Through pedigree analysis, three mothers carried a homozygous c.331C>T variant, which was a false-positive result. New primers were used, and this error was caused by allelic dropout. In this case, c.158G>A was likely a benign variant. Conclusions Sequence variants in primer-binding regions could cause allelic dropout, creating unpredictable errors in genotyping. Our results emphasised the need for careful measures to treat genotype–phenotype inconsistencies.


2022 ◽  
Vol 509 (1) ◽  
Author(s):  
Lê Thanh Hằng ◽  
Lê Thị Phương ◽  
Trần Huy Thịnh ◽  
Trần Vân Khánh
Keyword(s):  
Viet Nam ◽  

Bệnh α-thalassemia thường là gây nên là do đột biến xóa đoạn gen HBA1 và HBA2 làm thiếu hụt chuỗi α-globin cấu thành nên phân tử Hemoglobin. Tùy theo số lượng chuỗi α bị thiếu hụt mà mức độ biểu hiện lâm sàng của bệnh ở các cấp độ khác nhau. Xác định đột biến gen trên bệnh nhân sẽ giúp chẩn đoán xác định và tư vấn di truyền cho các thành viên gia đình bệnh nhân. Trong nghiên cứu này, kỹ thuật Multiplex Ligation-dependent Probe Amplification (MLPA) đã được áp dụng để xác định đột biến trên 21 bệnh nhân mắc bệnh α-thalassemia dựa vào các chỉ số huyết học, điện di huyết sắc tố và các dấu hiệu lâm sàng. Nghiên cứu đã xác định được 14/21 bệnh nhân mang kiểu gen --SEA/-ꭤ3.7, 7/21 bệnh nhân mang kiểu gen --SEA/-ꭤ4.2. MLPA là kỹ thuật khá hiệu quả để phát hiện các đột biến mất đoạn trên bệnh α thalassemia ở Việt Nam.


Author(s):  
Chanita Prapasrat ◽  
Preyaporn Onsod ◽  
Veerawat Korkiatsakul ◽  
Budsaba Rerkamnuaychoke ◽  
Duangrurdee Wattanasirichaigoon ◽  
...  

AbstractPrader–Willi syndrome (PWS) is a genetic disorder caused by the expression disruption of genes on the paternally inherited allele of chromosome 15q11.2-q13. Apart from clinical diagnostic criteria, PWS is confirmed by genetic testing. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) is one of the molecular techniques used to analyze this syndrome. This study aimed to evaluate the concordance of the test results of MS-MLPA with conventional techniques in the diagnosis of PWS in Thai patients. Forty leftover specimens from routine genetic testing (MS-PCR and FISH) were tested to obtain MS-MLPA results. By comparison, perfect concordance was shown between the result of MS-MLPA and those of conventional techniques. In conclusion, MS-MLPA is an accurate and cost-effective assay that can be used to confirm PWS diagnosis with explicit deletion of affected genes.


2021 ◽  
Vol 127 (24) ◽  
Author(s):  
Nastaran Dashti ◽  
Matteo Acciai ◽  
Sara Kheradsoud ◽  
Maciej Misiorny ◽  
Peter Samuelsson ◽  
...  

2021 ◽  
Vol 11 (11) ◽  
pp. 1232
Author(s):  
Elena Shakhtshneider ◽  
Dinara Ivanoshchuk ◽  
Olga Timoshchenko ◽  
Pavel Orlov ◽  
Sergey Semaev ◽  
...  

The aim of this work was to identify genetic variants potentially involved in familial hypercholesterolemia in 43 genes associated with lipid metabolism disorders. Targeted high-throughput sequencing of lipid metabolism genes was performed (80 subjects with a familial-hypercholesterolemia phenotype). For patients without functionally significant substitutions in the above genes, multiplex ligation-dependent probe amplification was conducted to determine bigger mutations (deletions and/or duplications) in the LDLR promoter and exons. A clinically significant variant in some gene associated with familial hypercholesterolemia was identified in 47.5% of the subjects. Clinically significant variants in the LDLR gene were identified in 19 probands (73.1% of all variants identified in probands); in three probands (11.5%), pathogenic variants were found in the APOB gene; and in four probands (15.4%), rare, clinically significant variants were identified in genes LPL, SREBF1, APOC3, and ABCG5. In 12 (85.7%) of 14 children of the probands, clinically significant variants were detectable in genes associated with familial hypercholesterolemia. The use of clinical criteria, targeted sequencing, and multiplex ligation-dependent probe amplification makes it possible to identify carriers of rare clinically significant variants in a wide range of lipid metabolism genes and to investigate their influence on phenotypic manifestations of familial hypercholesterolemia.


Andrologia ◽  
2021 ◽  
Author(s):  
Xiaoying Dai ◽  
Fu Shi ◽  
Cindy Ka Yee Cheung ◽  
Jue Li ◽  
Shengmou Lin
Keyword(s):  

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Rosa Barcelona-Cabeza ◽  
Walter Sanseverino ◽  
Riccardo Aiese Cigliano

Abstract Background Accurate copy number variant (CNV) detection is especially challenging for both targeted sequencing (TS) and whole‐exome sequencing (WES) data. To maximize the performance, the parameters of the CNV calling algorithms should be optimized for each specific dataset. This requires obtaining validated CNV information using either multiplex ligation-dependent probe amplification (MLPA) or array comparative genomic hybridization (aCGH). They are gold standard but time-consuming and costly approaches. Results We present isoCNV which optimizes the parameters of DECoN algorithm using only NGS data. The parameter optimization process is performed using an in silico CNV validated dataset obtained from the overlapping calls of three algorithms: CNVkit, panelcn.MOPS and DECoN. We evaluated the performance of our tool and showed that increases the sensitivity in both TS and WES real datasets. Conclusions isoCNV provides an easy-to-use pipeline to optimize DECoN that allows the detection of analysis-ready CNV from a set of DNA alignments obtained under the same conditions. It increases the sensitivity of DECoN without the need for orthogonal methods. isoCNV is available at https://gitlab.com/sequentiateampublic/isocnv.


2021 ◽  
Vol 9 ◽  
Author(s):  
Fenxia Li ◽  
Siping Liu ◽  
Bei Jia ◽  
Ruifeng Wu ◽  
Qingxian Chang

The Kagami–Ogata syndrome (KOS) is a rare imprinting disorder with a distinct clinical phenotype. In KOS, polyhydramnios is associated with a small bell-shaped thorax and coat-hanger ribs. The genetic etiology of KOS includes paternal uniparental disomy 14 [upd(14)pat], epimutations, and microdeletions affecting the maternally derived imprinted region of chromosome 14q32.2. More than 77 cases of KOS have been reported; however, only one mosaic upd(14)pat case has been reported. Here we report a second mosaic upd(14)pat case. The prognosis of upd(14)pat patients is poor because of severe respiratory insufficiency. We summarized prenatal ultrasound findings of KOS to raise awareness of this condition for possible diagnosis of KOS prenatally when polyhydramnios combination with a small bell-shaped thorax and other related features are first observed. Prenatal diagnosis using methylation-specific multiplex ligation-dependent probe amplification (MLPA) or a single-nucleotide polymorphism-based microarray analysis is recommended.


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