Article
Oncology
Seung-Hyun Jung, Hyeon-Chun Park, Youn Jin Choi, Sang Yong Song, Yeun-Jun Chung, Sug Hyung Lee
Summary: This study identified the histogenesis of GCTs through the analysis of single-nucleotide polymorphism array, revealing different genetic alterations between histologic areas within the same GCT. The findings suggest that GCTs may have various histogenesis and intratumoral genomic differences, which could be crucial for the identification of GCTs with different histologic areas.
JOURNAL OF PATHOLOGY
(2022)
Article
Genetics & Heredity
Yasuko Ogiwara, Mami Miyado, Erina Suzuki, Sumpei Niida, Kouichi Ozaki, Maki Fukami
Summary: The study investigated Y chromosomal variations in 160 Japanese men, revealing a high frequency and large inter-individual variability of AZF-linked CNVs and mLOY. The results demonstrate that AZF-linked CNVs do not increase the risk of aging-related mLOY.
JOURNAL OF HUMAN GENETICS
(2021)
Article
Biochemical Research Methods
Joseph T. Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick M. A. Sleiman, Hakon Hakonarson, Zhi Wei
Summary: Copy number variations (CNVs) are important in disease pathogenesis, but detection and validation remain challenging. DeepCNV, a deep learning-based tool, improves CNV call accuracy and reduces false positives and failures in CNV-disease association results.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Oncology
Marketa Wayhelova, Vladimira Vallova, Petr Broz, Aneta Mikulasova, Dominika Machackova, Hana Dynkova Filkova, Jan Smetana, Alena Takacsova, Renata Gaillyova, Petr Kuglik
Summary: The study reports a case of an infant with a congenital hypotrophy, short stature, and abnormal facial appearance, diagnosed with extremely rare cancer-predisposing Bloom syndrome. Trio-based exome sequencing revealed she carried a rare combination of causative sequence variants in the BLM gene, along with mosaic loss of heterozygosity of chromosome 11p. This case demonstrates the complexity and effectiveness of trio-based exome sequencing for molecular diagnostics of rare pediatric diseases.
MOLECULAR MEDICINE REPORTS
(2023)
Article
Immunology
Hao Sun, Zhan Yang, Zhihai Teng, Yanping Zhang, Zhenwei Han, Chao Xu, Zhu Wang, Hu Wang, Hongzhuang Wen, Xiaodong Chen, Changbao Qu, Yaxuan Wang
Summary: Sertoli cell -only syndrome (SCOS) is a type of testicular pathological failure that causes male infertility. The molecular mechanism underlying its development remains unknown. DDX58 has been identified as a key gene in SCOS, and its upregulation in SCOS testicular Sertoli cells is positively correlated with the expression of inflammatory factors. Mechanistically, DDX58 acts as an RNA-binding protein that enhances p65 expression by promoting mRNA stability. The DDX58/p65 regulatory axis might be a therapeutic target for SCOS.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Medicine, Research & Experimental
Victoria Spasova, Boris Mladenov, Simeon Rangelov, Zora Hammoudeh, Desislava Nesheva, Dimitar Serbezov, Rada Staneva, Savina Hadjidekova, Mihail Ganev, Lubomir Balabanski, Radoslava Vazharova, Chavdar Slavov, Draga Toncheva, Olga Antonova
Summary: This study aimed to detect copy number variations related to tumour progression and metastasis of urothelial carcinoma through whole-genome scanning. High-grade bladder tumours showed significant genetic imbalances in specific chromosomal regions, which may serve as potential targets for precision therapy.
EXPERIMENTAL AND THERAPEUTIC MEDICINE
(2021)
Article
Genetics & Heredity
K. Eggermann, R. Meyer, M. Begemann, D. Dey, E. Bueltmann, I Kurth, G. C. Korenke, C. Knopp
Summary: This study investigates the role of the SAMD9L gene in peripheral neuropathy and identifies a potentially pathogenic variant. The findings demonstrate that gain-of-function variants in this gene can lead to clinical symptoms associated with peripheral neuropathy.
Article
Dermatology
Q. Zhen, Y. Zhang, Y. Yu, H. Yang, T. Zhang, X. Li, X. Mo, B. Li, J. Wu, Y. Liang, H. Ge, Q. Xu, W. Chen, W. Qian, H. Xu, G. Chen, B. Bai, J. Zhang, Y. Lu, S. Chen, H. Zhang, X. Chen, X. Jin, X. Lin, L. Yong, M. Fang, J. Zhao, S. Wu, D. Jiang, J. Shi, H. Cao, Y. Qiu, S. Li, X. Kang, J. Shen, H. Ma, S. Sun, Y. Fan, M. Bai, Q. Jiang, W. Li, C. Lv, M. Chen, F. Li, Y. Li, L. Sun
Summary: The study identified novel structural variations (SVs) associated with psoriasis through genome-wide screening, enriching the understanding of the genetic architecture and pathogenesis of the disease. The impact of SVs on complex diseases, such as psoriasis, was highlighted, emphasizing the importance of considering SVs in genetic studies of complex diseases.
BRITISH JOURNAL OF DERMATOLOGY
(2022)
Article
Multidisciplinary Sciences
Yu Chen, Amy Y. Wang, Courtney A. Barkley, Yixin Zhang, Xinyang Zhao, Min Gao, Mick D. Edmonds, Zechen Chong
Summary: The authors developed DeBreak, an algorithm for comprehensive and accurate structural variant (SV) detection in long-read sequencing data, which outperforms existing SV callers.
NATURE COMMUNICATIONS
(2023)
Article
Biotechnology & Applied Microbiology
Kangqi Lv, Dayang Chen, Dan Xiong, Huamei Tang, Tong Ou, Lijuan Kan, Xiuming Zhang
Summary: This study developed a functional deleteriousness-based model of CNV (dbCNV) to predict the pathogenicity of CNVs and provide a deeper understanding of the pathogenic mechanism.
Article
Neurosciences
Kamila Szecowka, Blazej Misiak, Izabela Laczmanska, Dorota Frydecka, Ahmed A. Moustafa
Summary: Schizophrenia is a neurodevelopmental disorder influenced by genetic and environmental factors. Understanding the genetic liability contributing to schizophrenia could lead to improved therapy and new treatment methods. Research focuses on genetic variants, such as copy number variations (CNVs) or single-nucleotide variants (SNVs). Certain CNVs, such as those associated with 22q11.2 microdeletion syndrome or 1q21.1 microduplication/microdeletion syndrome, increase the risk of developing schizophrenia. This article provides a unifying framework linking these CNVs and associated genetic disorders to schizophrenia and its various neural and behavioral abnormalities.
MOLECULAR NEUROBIOLOGY
(2023)
Article
Oncology
Jan Barinka, Zunsong Hu, Lu Wang, David A. Wheeler, Delaram Rahbarinia, Clay McLeod, Zhaohui Gu, Charles G. Mullighan
Summary: In this study, the authors describe a method called RNAseqCNV for detecting CNVs from RNA-seq data. They used models based on gene expression and minor allele frequency to accurately classify CNVs in ALL and AML. The results showed that RNAseqCNV outperforms other algorithms in detecting CNVs in the ALL dataset and the calls were highly concordant with DNA-based CNV results.
Article
Biotechnology & Applied Microbiology
Jinsheng Xu, Weihan Zhang, Ping Zhang, Weicheng Sun, Yuepeng Han, Li Li
Summary: This study identified 914,610 CNVs and 14,839 CNVRs from 346 apple accessions. CNVRs accounted for 10.03% of the apple genome and accurately reflected the population structure of apple. The CNVRs covered 3,621 genes involved in biological processes and identified 127 CN-differentiated genes that may contribute to trait differences between cultivars and wild relatives.
Article
Cell Biology
Yaxi Xu, Jian Hu, Wenlei Fan, Hehe Liu, Yunsheng Zhang, Zhanbao Guo, Wei Huang, Xiaolin Liu, Shuisheng Hou
Summary: This study discovered the existence of variations in the number of cervical vertebrae in duck populations. Most ducks had 15 cervical vertebrae, while a small number had 14 or 16. The number of cervical vertebrae had a positive influence on neck production, with each additional cervical vertebra resulting in an increase of 11 g or 2 cm in duck neck length. Through genome-wide analysis, six copy number variations (CNVs) associated with the number of cervical vertebrae were identified, with the associated CNV regions containing 15 genes including WNT10A and WNT6. These findings are important for understanding variations in the number of vertebrae in ducks and provide a foundation for future duck breeding.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Agriculture, Dairy & Animal Science
Rosalia Di Gerlando, Salvatore Mastrangelo, Marco Tolone, Ilaria Rizzuto, Anna Maria Sutera, Angelo Moscarelli, Baldassare Portolano, Maria Teresa Sardina
Summary: The aim of this study was to identify CNVs and perform a CNV-based population genetics analysis in five Italian sheep breeds. The results showed that the five breeds tend to cluster in distinct groups, and gene enrichment analysis revealed genes involved in lipid metabolism, immune response, and the olfactory pathway.
Article
Immunology
Amanpreet Kaur Kalsi, Ashutosh Halder, Manish Jain, Pradeep K. Chaturvedi, Mary Mathew, Jai Bhagwan Sharma
AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY
(2019)
Article
Biochemistry & Molecular Biology
Shivali Jasrotia, Ritu Gupta, Atul Sharma, Ashutosh Halder, Lalit Kumar
Article
Cell Biology
Manisha Singh, Manish Jain, Samrat Bose, Ashutosh Halder, Tapas Chandra Nag, Amit Kumar Dinda, Sujata Mohanty
Summary: This study investigated the neurogenic effect of 22(R)-hydroxycholesterol on human mesenchymal stem cells derived from bone marrow, adipose tissue, and dental pulp, as well as explored their regenerative potential. Results showed that dental pulp-derived MSCs had the greatest regenerative effect post-transplantation, indicating a potential for future therapeutic use in treating Parkinson's disease.
CELL DEATH DISCOVERY
(2021)
Article
Cell Biology
Divya Aggarwal, Neelam Wadhwa, Tanvi Arora, Shalini Rajaram, Preeti Diwaker, Ashutosh Halder, Manish Jain, Kiran Mishra
Summary: The study explored the correlation between hTERC gene expression and chromosome 7 ploidy with worsening cytological and histological outcomes in cervical squamous carcinogenesis. It found significant positive associations for both genetic aberrations, indicating their potential relevance in settings of discrepant cytology-histology correlation. High-grade lesions had significantly higher results compared to under- or overdiagnosed cases on cytology.
Article
Reproductive Biology
Ashutosh Halder, Isha Chaudhary, Manish Jain, Shivam Pandey
Summary: In a homogeneous population of mice, skewed sex ratios were observed in preimplantation and post-implantation embryos, with a reversal skewing at birth. A high-fat diet promoted male sex ratio at birth, suggesting selective elimination of female embryos and fetuses throughout pregnancy in mice, especially with a high-fat diet.
REPRODUCTIVE BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Neha Kaushik, Soumya Rastogi, Sonia Verma, Deepak Pandey, Ashutosh Halder, Arnab Mukhopadhyay, Neeraj Kumar
Summary: In C. elegans, reduced insulin signaling (rIIS) leads to differential regulation of target genes by the transcription factors DAF-16/FOXO, SKN-1/Nrf-1, and HSF1/HSF-1. DAF-16 acts primarily as an activator under rIIS, while SKN-1 and HSF-1 function as both activators and repressors. Regardless of activation or repression, DAF-16 is the principal determining factor for genes commonly regulated by TFs under rIIS conditions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, General & Internal
Hemant Kumar, Ashutosh Halder, Mona Sharma, Manish Jain, Amanpreet Kaur Kalsi
Summary: The study aimed to evaluate different androgens in PCOS women from north India to determine the best available biomarker. The results showed that Dihydrotestosterone (DHT) can be considered as a diagnostic biomarker of hyperandrogenemia in PCOS women from north India.
JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH
(2022)
Meeting Abstract
Oncology
Prasanth Srinivasan, Jagdish Prasad Meena, Aditya Gupta, Ashutosh Halder, Arti Kapil, Rm Pandey, Rachna Seth
PEDIATRIC BLOOD & CANCER
(2022)
Article
Medicine, General & Internal
Amanpreet Kaur Kalsi, Ashutosh Halder, Manish Jain, Amita Srivastava
JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH
(2020)
Article
Medicine, General & Internal
Isha Rishi, Ashutosh Halder, J. B. Sharma, Manish Jain, Mona Sharma
JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH
(2020)
Article
Pathology
Pragya Jain, Neelam Wadhwa, Mohit K. Joshi, Manish Jain, Ashutosh Halder, Kiran Mishra
INDIAN JOURNAL OF PATHOLOGY AND MICROBIOLOGY
(2020)
Article
Endocrinology & Metabolism
Amanpreet Kaur Kalsi, Ashutosh Halder, Manish Jain, P. K. Chaturvedi, J. B. Sharma
Article
Medicine, General & Internal
Ashutosh Halder, Manish Jain, Amanpreet Kaur Kalsi
JOURNAL OF CLINICAL AND DIAGNOSTIC RESEARCH
(2018)
Article
Andrology
P. Kumar, M. Jain, A. K. Kalsi, A. Halder
Article
Genetics & Heredity
Xiangge Meng, Chengping Li, Yu Hei, Xiang Zhou, Guoli Zhou
Summary: The study used IVT-SAPAS sequencing to analyze the dynamic changes of APA sites during adipogenesis in bovine subcutaneous preadipocytes and intramuscular preadipocytes. The results showed that APA plays an important role in adipocyte differentiation, and UTR-APA switching genes have different trends, with intramuscular preadipocytes tending to use shorter 3'UTR for differentiation. TRIB3, WWTR1, and INSIG1 play important roles in intramuscular preadipocyte differentiation.
Article
Genetics & Heredity
S. Alizadeh, S. Khamse, N. Tajeddin, H. R. Khorram Khorshid, A. Delbari, M. Ohadi
Summary: This study identifies a specific genotype at a CG-rich trinucleotide short tandem repeat (STR) locus that is associated with late-onset neurocognitive disorders such as Alzheimer's disease (AD).
Article
Genetics & Heredity
Shougang Liu, Zhe Zhuang, Fanghua Liu, Xiuqing Yuan, Zeqiao Zhang, Xiaoqian Liang, Xinhui Li, Yongfeng Chen
Summary: This study investigated the effect and mechanism of RPL9 and TIFA in scalp psoriasis, and identified RPL9 as a potential therapeutic target for scalp psoriasis.
Article
Genetics & Heredity
Shiting Wang, Jiaqi Chen, Zhichao Jin, Ying Xing, Ruiping Wang
Summary: This study suggests a causal association between hair color and skin cancers, with light hair colors (red, blonde, and light brown) being associated with an increased risk and dark brown hair being associated with a decreased risk.
Article
Genetics & Heredity
Joseph Hawadak, Loick Pradel Kojom Foko, Rodrigue Roman Dongang Nana, Karmveer Yadav, Veena Pande, Aparup Das, Vineeta Singh
Summary: This study investigates the genetic diversity and natural selection of the Pfama-1 gene in Plasmodium falciparum isolates from Cameroon. The study finds a considerable nucleotide and haplotype diversity, as well as specific mutations in Cameroonian isolates. Positive diversifying selection and the identification of selected codon sites suggest the potential implication of these genetic variations in host immune pressure and parasite-binding complex modulation. The findings provide valuable baseline data for malaria vaccine design.
Article
Genetics & Heredity
Emily Biernat, Mansi Verma, Chhabi K. Govind
Summary: RSC is an essential ATP-dependent chromatin remodeling complex in Saccharomyces cerevisiae. It regulates nucleosome-depleted regions (NDRs) by sliding flanking nucleosomes away from NDRs. Depletion of RSC leads to nucleosome encroachment in NDRs and transcription initiation defects. The study compared the effects of catalytic-dead Sth1 and rapid depletion of Sth1 on transcription. Rapid depletion of Sth1 reduces recruitment of TBP and Pol II, while the catalytic-dead mutant exhibits a severe reduction in TBP binding but accumulates Pol II in coding regions. The results suggest a role for RSC in transcription elongation and termination processes.
Article
Genetics & Heredity
Yunxiao Wei, Yuhan Song, Muhammad Aamir Khan, Chengzhen Liang, Zhigang Meng, Yuan Wang, Sandui Guo, Rui Zhang
Summary: This study analyzed the GhTPP protein family in upland cotton for the first time and identified the important role of GhTPPA_2 in regulating sugar metabolism, improving soluble sugar accumulation, and drought stress tolerance.
Article
Genetics & Heredity
Yannan Geng, Rui Shao, Tiantong Xu, Lilong Zhang
Summary: A novel risk model based on SCUBE3, TNNC1, SPON1, SEPT12 and ULBP1 genes was developed for predicting PMOP risk, with higher risk score indicating higher risk of suffering from PMOP. Significant differences in signaling pathway activities were observed between the high-risk score group and the low-risk score group.
Article
Genetics & Heredity
Randy P. Williams, Corina Lesseur, Haoxiang Cheng, Qian Li, Maya Deyssenroth, Christopher D. Molteno, Ernesta M. Meintjes, Sandra W. Jacobson, Joseph L. Jacobson, Helen Wainwright, Ke Hao, Jia Chen, R. Colin Carter
Summary: The study suggests that heavy alcohol exposure during pregnancy may impact the proportion of fetal placental villi macrophages and increase the expression of inflammatory genes. Further research is needed to explore these effects and evaluate the potential functional roles of placental inflammation in FASD.
Article
Genetics & Heredity
Lvjing Luo, Lishuang Sun, Shu Li, Huiting Liu, Zhengyu Chen, Shi Huang, Yinyin Mo, Genliang Li
Summary: This study analyzed the expression of Ptpn1 and miR-124-3p in testicular tissues of mice and investigated their regulatory relationship. The results showed that Ptpn1 expression was up-regulated in adult mouse testis compared to juvenile mouse testis, while miR-124-3p expression showed an opposite pattern. Further analysis suggested that the down-regulation of miR-124-3p may contribute to the high expression of Ptpn1 in adult mouse testis.
Article
Genetics & Heredity
Gairui Li, Dan Zhao, Xiaolin Peng, Yashuang Zhao
Summary: MiRNA-22 shows potential as a candidate for early diagnosis of colorectal cancer (CRC). The study found higher miR-22 expression levels in the CRC and CRA groups, suggesting its potential as a biomarker for CRC early screening.
Article
Genetics & Heredity
Zhongqiu Zhu, Qianting Yang, Xiaoying Tian, Da Man, Jian Wang, Junfang Zhang, Bingshe Han
Summary: This study constructed a ceRNA network mediated by lncRNAs in cold-acclimated zebrafish ZF4 cells and revealed that upregulation of MSTRG3207 promotes apoptosis by sponging dre-miR-736 during cold acclimation.
Article
Genetics & Heredity
Weitao Chen, Denggao Xiang, Shang Gao, Shuli Zhu, Zhi Wu, Yuefei Li, Jie Li
Summary: Dam construction has negatively impacted the genetic diversity and structure of fish populations. This case study on the endangered Hemibagrus guttatus found low genetic diversity, high levels of inbreeding, and decreasing population size in fragmented populations. Genetic structure and differentiation were also observed, indicating the influence of dams on these fish populations.
Article
Genetics & Heredity
Pooja Singh, Debleena Guin, Bijay Pattnaik, Ritushree Kukreti
Summary: Through systematic literature review and meta-analysis, it was found that idiopathic pulmonary fibrosis is significantly associated with 222 polymorphisms in 118 genes. Four polymorphisms - rs35705950/MUC5B, rs2736100/TERT, rs2076295/DSP, and rs111521887/TOLLIP, exhibited substantial epidemiological evidence supporting their association with IPF risk.
Article
Genetics & Heredity
Jianping Zhang, Zhijun Cai, Fanzhe Feng, Yufeng Peng, Yi Cui, Yongiqing Xu
Summary: This study found that exosomes secreted by young BMSCs can promote the healing of tendon-bone interface after rotator cuff tears. These exosomes can improve extracellular matrix remodeling, osteogenic differentiation, angiogenesis, and stemness of tendon-derived stem cells (TDSCs). The exosomes from young BMSCs have better effects compared to those from aged BMSCs.