Mutational Spectrum Analysis of Seven Genes Associated with Thyroid Dyshormonogenesis

Objective. Thyroid dyshormonogenesis (DH) is a genetically heterogeneous inherited disorder caused by thyroid hormone synthesis abnormalities. This study aims at comprehensively characterizing the mutation spectrum in Chinese patients with DH. Subjects and Methods. We utilized next-generation sequencing to screen for mutations in seven DH-associated genes (TPO, DUOX2, TG, DUOXA2, SLC26A4, SLC5A5, and IYD) in 21 Chinese Han patients with DH from Xinjiang Province. Results. Twenty-eight rare nonpolymorphic variants were found in 19 patients (90.5%), including 19, 5, 3, and 1 variants in DUOX2, TG, DUOXA2, and SLC26A4, respectively. Thirteen (62%) patients carried monogenic mutations, and six (28.5%) carried oligogenic mutations. Fifteen (71%) patients carried 2 or more DUOX2 (14) or DUOXA2 (1) variants. The genetic basis of DH in nine (43%) patients harboring biallelic or triallelic pathogenic variants was resolved. Seventeen patients (81%) carried DUOX2 mutations, most commonly p.R1110Q or p.K530X. No correlations were found between DUOX2 mutation types or numbers and clinical phenotypes. Conclusions. DUOX2 mutations were the most predominant genetic alterations of DH in the study cohort. Oligogenicity may explain the genetic basis of disease in many DH patients. Functional studies and further clinical studies with larger DH patient cohorts are needed to validate the roles of the mutations identified in this study.

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Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms

Cancers ◽

10.3390/cancers11091364 ◽

2019 ◽

Vol 11 (9) ◽

pp. 1364 ◽

Cited By ~ 6

Author(s):

Diego Carbonell ◽

Julia Suárez-González ◽

María Chicano ◽

Cristina Andrés-Zayas ◽

Juan Carlos Triviño ◽

...

Keyword(s):

Next Generation Sequencing ◽

Copy Number Variants ◽

Genetic Alterations ◽

Next Generation ◽

Pathogenic Variants ◽

Myeloid Neoplasms ◽

Diagnostic Samples ◽

Gene Panels ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.

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Genomic profiling of Chinese patients with urothelial carcinoma

BMC Cancer ◽

10.1186/s12885-021-07829-1 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Bo Yang ◽

Xiao Zhao ◽

Chong Wan ◽

Xin Ma ◽

Shaoxi Niu ◽

...

Keyword(s):

Urothelial Carcinoma ◽

Tumor Tissue ◽

Genetic Alterations ◽

Chinese Patients ◽

Study Cohort ◽

Genomic Feature ◽

Genomic Alterations ◽

Tissue Samples ◽

Genomic Features ◽

Somatic Alterations

Abstract Backgrounds Urothelial carcinoma (UC) is the most common genitourinary malignancy in China. In this study, we surveyed the genomic features in Chinese UC patients and investigated the concordance of genetic alterations between circulating tumor DNA (ctDNA) in plasma and matched tumor tissue. Materials and methods A total of 112 UC patients were enrolled, of which 31 were upper tract UC (UTUC) and 81 were UC of bladder (UCB). Genomic alterations in 92 selected genes were analyzed by targeted next-generation sequencing. Results In the study cohort, 94.64, 86.61 and 62.50% of patients were identified as having valid somatic, oncogenic and actionable somatic alterations, respectively. The most frequently altered genes included TP53, KMT2D, KDM6A, FAT4, FAT1, CREBBP and ARID1A. The higher prevalence of HRAS (22.0% vs 3.7%) and KMT2D (59.26% vs 34.57%) was identified in UTUC than in UCB. Comparisons of somatic alterations of UCB and UTUC between the study cohort and western cohorts revealed significant differences in mutant prevalence. Notably, 28.57, 17.86 and 47.32% of the cases harbored alterations in FGFRs, ERBBs and DNA damage repair genes, respectively. Furthermore, 75% of the patients carried non-benign germline variants, but only two (1.79%) were pathogenic. The overall concordance for genomic alterations in ctDNA and matched tumor tissue was 42.97% (0–100%). Notably, 47.25% of alterations detected in ctDNA were not detected in the matched tissue, and 54.14% of which were oncogenic mutations. Conclusions We found a unique genomic feature of Chinese UC patients. A reasonably good concordance of genomic features between ctDNA and tissue samples were identified.

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Novel mutations identified in the Chinese Han population with keratoconus by next-generation sequencing

10.21203/rs.3.rs-121907/v1 ◽

2020 ◽

Author(s):

Binbin Chen ◽

Xiaoning Yu ◽

Xin Zhang ◽

Hao Yang ◽

Yilei Cui ◽

...

Keyword(s):

Next Generation Sequencing ◽

Chinese Han Population ◽

Chinese Patients ◽

Genome Wide Association Studies ◽

Next Generation ◽

Sequencing Technology ◽

Novel Mutations ◽

Chinese Han ◽

Han Population ◽

Generation Sequencing

Abstract BACKGROUND Keratoconus (KC) is characterized by bilateral progressive corneal thinning and ectasia. The prevalence of KC is approximately 8.8 to 54.4 per 100,000 individuals across the globe. Genetic factors have been shown to contribute to the pathogenesis of KC. This study will identify new mutations in the susceptibility gene of keratoconus (KC) in the Chinese Han population. METHODS A total of fifty-two patients with primary KC were recruited. Blood samples were collected, and genomic DNA was isolated from peripheral blood leukocytes. The entire coding region, intron–exon junctions, and promoter regions of sixteen known KC susceptibility genes were screened with next-generation sequencing technology, and all identified variants were further confirmed using the Sanger sequencing technology. The Sorting Intolerant from Tolerant (SIFT), Mutation Taster and PolyPhen 2 programs were used to predict the effect of amino acid substitution on protein. RESULTS After removing twelve known SNPs (single nucleotide polymorphisms) and three variants predicted to be harmless, nine novel mutations were identified in eight of the fifty-two patients, including c.455C > T:p.P152L in FNDC3B, c.3636_3637del:p.R1212fs in COL4A4, c.5015G > T:p.R1672L, c.3798dupA:p.P1267fs and c.28G > A:p.A10T in MPDZ, c.1940C > T:p.P647L in DOCK9, c.127_128insGGC:p.Q43delinsRQ in POLG, c.3019G > A:p.V1007I in IPO5, and c.624 + 7->A in TGFBI. All nine mutations in the patients with KC were heterozygote. CONCLUSION This study enlarged the gene profile of KC and should be further confirmed by well-powered, genome-wide association studies (GWAS) of Han Chinese patients.

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A Novel Likely Pathogenic Variant in the BLOC1S5 Gene Associated with Hermansky-Pudlak Syndrome Type 11 and an Overview of Human BLOC-1 Deficiencies

Cells ◽

10.3390/cells10102630 ◽

2021 ◽

Vol 10 (10) ◽

pp. 2630

Author(s):

Doris Boeckelmann ◽

Mira Wolter ◽

Barbara Käsmann-Kellner ◽

Udo Koehler ◽

Lea Schieber-Nakamura ◽

...

Keyword(s):

Genetic Defect ◽

Adaptor Protein ◽

Genetic Alterations ◽

Oculocutaneous Albinism ◽

Pathogenic Variants ◽

New Type ◽

Hermansky Pudlak Syndrome ◽

Lysosome Related Organelles ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Hermansky-Pudlak syndrome (HPS) is a heterogeneous disorder combining oculocutaneous albinism (OCA) and a platelet function disorder of varying severity as its most prominent features. The genes associated with HPS encode for different BLOC- (biogenesis of lysosome-related organelles complex) complexes and for the AP-3 (adaptor protein-3) complex, respectively. These proteins are involved in maturation, trafficking, and the function of lysosome-related organelles (LROs) such as melanosomes and platelet δ-granules. Some patients with different types of HPS can develop additional complications and symptoms like pulmonary fibrosis, granulomatous colitis, and immunodeficiency. A new type of HPS has recently been identified associated with genetic alterations in the BLOC1S5 gene, which encodes the subunit Muted of the BLOC-1 complex. Our aim was to unravel the genetic defect in two siblings with a suspected HPS diagnosis (because of OCA and bleeding symptoms) using next generation sequencing (NGS). Platelet functional analysis revealed reduced platelet aggregation after stimulation with ADP and a severe secretion defect in platelet δ-granules. NGS identified a novel homozygous essential splice site variant in the BLOC1S5 gene present in both affected siblings who are descendants of a consanguine marriage. The patients exhibited no additional symptoms. Our study confirms that pathogenic variants of BLOC1S5 cause the recently described HPS type 11.

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A hemizygous p.R204Q mutation in the ALAS2 gene underlies X-linked sideroblastic anemia in an adult Chinese Han man

BMC Medical Genomics ◽

10.1186/s12920-021-00950-x ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Jinbo Huang ◽

Meili Ge ◽

Yingqi Shao ◽

Min Wang ◽

Peng Jin ◽

...

Keyword(s):

Genetic Basis ◽

Clinical Manifestations ◽

Hypochromic Anemia ◽

Hereditary Disease ◽

Chinese Family ◽

Chinese Han ◽

Sideroblastic Anemia ◽

Aminolevulinate Synthase ◽

Male Patients ◽

Generation Sequencing

Abstract Background X-linked sideroblastic anemia (XLSA) is the most common form of congenital sideroblastic anemia (CSA), and is associated with the mutations in the 5-aminolevulinate synthase 2 (ALAS2). The genetic basis of more than 40% of CSA cases remains unknown. Methods A two-generation Chinese family with XLSA was studied by next-generation sequencing to identify the underlying CSA-related mutations. Results In the study, we identified a missense ALAS2 R204Q mutation in a hemizygous Chinese Han man and in his heterozygous daughter. The male proband presented clinical manifestations at 38 years old and had a good response to pyridoxine. Conclusions XLSA, as a hereditary disease, can present clinical manifestations later in lives, for adult male patients with ringed sideroblasts and hypochromic anemia, it should be evaluated with gene analyses to exclude CSA.

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Update on Genetic Basis of Brugada Syndrome: Monogenic, Polygenic or Oligogenic?

International Journal of Molecular Sciences ◽

10.3390/ijms21197155 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7155 ◽

Cited By ~ 1

Author(s):

Oscar Campuzano ◽

Georgia Sarquella-Brugada ◽

Sergi Cesar ◽

Elena Arbelo ◽

Josep Brugada ◽

...

Keyword(s):

Brugada Syndrome ◽

Genetic Basis ◽

Rare Variants ◽

Genetic Diagnosis ◽

Genetic Alterations ◽

Pathogenic Variants ◽

Oligogenic Inheritance ◽

The Many ◽

Scn5a Gene

Brugada syndrome is a rare inherited arrhythmogenic disease leading to ventricular fibrillation and high risk of sudden death. In 1998, this syndrome was linked with a genetic variant with an autosomal dominant pattern of inheritance. To date, rare variants identified in more than 40 genes have been potentially associated with this disease. Variants in regulatory regions, combinations of common variants and other genetic alterations are also proposed as potential origins of Brugada syndrome, suggesting a polygenic or oligogenic inheritance pattern. However, most of these genetic alterations remain of questionable causality; indeed, rare pathogenic variants in the SCN5A gene are the only established cause of Brugada syndrome. Comprehensive analysis of all reported genetic alterations identified the origin of disease in no more than 40% of diagnosed cases. Therefore, identifying the cause of this rare arrhythmogenic disease in the many families without a genetic diagnosis is a major current challenge in Brugada syndrome. Additional challenges are interpretation/classification of variants and translation of genetic data into clinical practice. Further studies focused on unraveling the pathophysiological mechanisms underlying the disease are needed. Here we provide an update on the genetic basis of Brugada syndrome.

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Next Generation Sequencing Reveals Pathogenic and Actionable Genetic Alterations of Soft Tissue Sarcoma in Chinese Patients: A Single Center Experience

Technology in Cancer Research & Treatment ◽

10.1177/15330338211068964 ◽

2021 ◽

Vol 20 ◽

pp. 153303382110689

Author(s):

Gu Jin ◽

Chunyang Wang ◽

Dongdong Jia ◽

Wenkang Qian ◽

Chunming Yin ◽

...

Keyword(s):

Next Generation Sequencing ◽

Soft Tissue ◽

Soft Tissue Sarcoma ◽

Genetic Alterations ◽

Chinese Patients ◽

Clinical Test ◽

Next Generation ◽

Single Center ◽

Single Center Experience ◽

Generation Sequencing

Background: Next generation sequencing (NGS) has systematically investigated the genomic landscape of soft tissue sarcoma (STS) in Western patients, but few reports have described the utility of NGS in identifying pathogenic and targetable mutations in Asian patients. Methods: We review our single center experience of identifying the genomic profile and feasible genetic mutations in 65 Chinese patients with STS by NGS. Results: On average, 3.35 mutations were identified per patient (range, 0-28), and at least one mutation could be detected in 95.4% (62/65) of patients. TP53, MDM2, CDK4, KDR, and NF1 were the most frequent mutation genes in Chinese STS patients. Actionable mutations were discovered in 36.9% (24/65) of patients, and clinical benefit was achieved in 4 patients treated with corresponding molecular targeted therapies. Conclusions: Our study describes the mutation profile of Chinese STS patients by a single center experience. Some patients have achieved improved clinical outcomes by adopting treatment based on the results of genetic testing. NGS may affect clinical decision-making as a routine clinical test for patients with STS.

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Phenotypic Variability of Patients With PAX8 Variants Presenting With Congenital Hypothyroidism and Eutopic Thyroid

The Journal of Clinical Endocrinology & Metabolism ◽

10.1210/clinem/dgaa711 ◽

2020 ◽

Vol 106 (1) ◽

pp. e152-e170

Author(s):

Núria Camats ◽

Noelia Baz-Redón ◽

Mónica Fernández-Cancio ◽

María Clemente ◽

Ariadna Campos-Martorell ◽

...

Keyword(s):

Thyroid Hormone ◽

Thyroid Gland ◽

Congenital Hypothyroidism ◽

Phenotypic Variability ◽

Hereditary Diseases ◽

Hormone Synthesis ◽

Functional Studies ◽

Thyroid Hormone Synthesis ◽

Thyroid Dyshormonogenesis

Abstract Purpose Thyroid dyshormonogenesis is a heterogeneous group of hereditary diseases produced by a total/partial blockage of the biochemical processes of thyroid-hormone synthesis and secretion. Paired box 8 (PAX8) is essential for thyroid morphogenesis and thyroid hormone synthesis. We aimed to identify PAX8 variants in patients with thyroid dyshormonogenesis and to analyze them with in vitro functional studies. Patients and Methods Nine pediatric patients with a eutopic thyroid gland were analyzed by the Catalan screening program for congenital hypothyroidism. Scintigraphies showed absent, low, or normal uptake. Only one patient had a hypoplastic gland. On reevaluation, perchlorate discharge test was negative or compatible with partial iodine-organization deficit. After evaluation, 8 patients showed permanent mild or severe hypothyroidism. Massive-sequencing techniques were used to detect variants in congenital hypothyroidism-related genes. In vitro functional studies were based on transactivating activity of mutant PAX8 on a TG-gene promoter and analyzed by a dual-luciferase assays. Results We identified 7 heterozygous PAX8 exonic variants and 1 homozygous PAX8 splicing variant in 9 patients with variable phenotypes of thyroid dyshormonogenesis. Five were novel and 5 variants showed a statistically significant impaired transcriptional activity of TG promoter: 51% to 78% vs the wild type. Conclusions Nine patients presented with PAX8 candidate variants. All presented with a eutopic thyroid gland and 7 had deleterious variants. The phenotype of affected patients varies considerably, even within the same family; but, all except the homozygous patient presented with a normal eutopic thyroid gland and thyroid dyshormonogenesis. PAX8 functional studies have shown that 6 PAX8 variants are deleterious. Our studies have proven effective in evaluating these variants.

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Whole-exome sequencing of a large Chinese azoospermia and severe oligospermia cohort identifies novel infertility causative variants and genes

Human Molecular Genetics ◽

10.1093/hmg/ddaa101 ◽

2020 ◽

Vol 29 (14) ◽

pp. 2451-2459

Author(s):

Shitao Chen ◽

Guishuan Wang ◽

Xiaoguo Zheng ◽

Shunna Ge ◽

Yubing Dai ◽

...

Keyword(s):

Exome Sequencing ◽

Whole Exome Sequencing ◽

Molecular Characteristics ◽

Obstructive Azoospermia ◽

Sequencing Data ◽

Chinese Han ◽

Functional Studies ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Whole Exome

Abstract Rare coding variants have been proven to be one of the significant factors contributing to spermatogenic failure in patients with non-obstructive azoospermia (NOA) and severe oligospermia (SO). To delineate the molecular characteristics of idiopathic NOA and SO, we performed whole-exome sequencing of 314 unrelated patients of Chinese Han origin and verified our findings by comparing to 400 fertile controls. We detected six pathogenic/likely pathogenic variants and four variants of unknown significance, in genes known to cause NOA/SO, and 9 of which had not been earlier reported. Additionally, we identified 20 novel NOA candidate genes affecting 25 patients. Among them, five (BRDT, CHD5, MCM9, MLH3 and ZFX) were considered as strong candidates based on the evidence obtained from murine functional studies and human single-cell (sc)RNA-sequencing data. These genetic findings provide insight into the aetiology of human NOA/SO and pave the way for further functional analysis and molecular diagnosis of male infertility.

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ISSAID/EMQN Best Practice Guidelines for the Genetic Diagnosis of Monogenic Autoinflammatory Diseases in the Next-Generation Sequencing Era

Clinical Chemistry ◽

10.1093/clinchem/hvaa024 ◽

2020 ◽

Vol 66 (4) ◽

pp. 525-536 ◽

Cited By ~ 4

Author(s):

Yael Shinar ◽

Isabella Ceccherini ◽

Dorota Rowczenio ◽

Ivona Aksentijevich ◽

Juan Arostegui ◽

...

Keyword(s):

Next Generation Sequencing ◽

Best Practice ◽

Copy Number Variants ◽

Genetic Diagnosis ◽

Genetic Alterations ◽

Autoinflammatory Diseases ◽

Next Generation ◽

Disease Category ◽

Pathogenic Variants ◽

Generation Sequencing

Abstract Background Monogenic autoinflammatory diseases are caused by pathogenic variants in genes that regulate innate immune responses, and are characterized by sterile systemic inflammatory episodes. Since symptoms can overlap within this rapidly expanding disease category, accurate genetic diagnosis is of the utmost importance to initiate early inflammation-targeted treatment and prevent clinically significant or life-threatening complications. Initial recommendations for the genetic diagnosis of autoinflammatory diseases were limited to a gene-by-gene diagnosis strategy based on the Sanger method, and restricted to the 4 prototypic recurrent fevers (MEFV, MVK, TNFRSF1A, and NLRP3 genes). The development of best practices guidelines integrating critical recent discoveries has become essential. Methods The preparatory steps included 2 online surveys and pathogenicity annotation of newly recommended genes. The current guidelines were drafted by European Molecular Genetics Quality Network members, then discussed by a panel of experts of the International Society for Systemic Autoinflammatory Diseases during a consensus meeting. Results In these guidelines, we combine the diagnostic strength of next-generation sequencing and recommendations to 4 more recently identified genes (ADA2, NOD2, PSTPIP1, and TNFAIP3), nonclassical pathogenic genetic alterations, and atypical phenotypes. We present a referral-based decision tree for test scope and method (Sanger versus next-generation sequencing) and recommend on complementary explorations for mosaicism, copy-number variants, and gene dose. A genotype table based on the 5-category variant pathogenicity classification provides the clinical significance of prototypic genotypes per gene and disease. Conclusions These guidelines will orient and assist geneticists and health practitioners in providing up-to-date and appropriate diagnosis to their patients.

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