Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics.

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Colorectal cancer (CRC) is one of the major causes of cancer deaths across the world. Patients’ survival at time of diagnosis depends mainly on stage of the tumor. Therefore, understanding the molecular mechanisms from low-grade to high-grade stages of cancer that lead to cellular migration from one tissue/organ to another tissue/organ is essential for implementing therapeutic approaches. To this end, we performed a unique meta-analysis flowchart by identifying differentially expressed genes (DEGs) between normal, primary (primary sites), and metastatic samples (Colorectal metastatic lesions in liver and lung) in some Test datasets. DEGs were employed to construct a protein-protein interaction (PPI) network. A smaller network containing 39 DEGs was then extracted from the PPI network whose nodes expression induction or suppression alone or in combination with each other would inhibit tumor progression or metastasis. These DEGs were then verified by gene expression profiling, survival analysis, and multiple Validation datasets. We suggested for the first time that downregulation of mitochondrial genes, including ETHE1, SQOR, TST, and GPX3, would help colorectal cancer cells to produce more energy under hypoxic conditions through mechanisms that are different from “Warburg Effect”. Augmentation of given antioxidants and repression of P4HA1 and COL1A2 genes could be a choice of CRC treatment. Moreover, promoting active GSK-3β together with expression control of EIF2B would prevent EMT. We also proposed that OAS1 expression enhancement can induce the anti-cancer effects of interferon-gamma, while suppression of CTSH hinders formation of focal adhesions. ATF5 expression suppression sensitizes cancer cells to anchorage-dependent death signals, while LGALS4 induction recovers cell-cell junctions. These inhibitions and inductions would be another combinatory mechanism that inhibits EMT and cell migration. Furthermore, expression inhibition of TMPO, TOP2A, RFC3, GINS1, and CKS2 genes could prevent tumor growth. Besides, TRIB3 suppression would be a promising target for anti−angiogenic therapy. SORD is a poorly studied enzyme in cancer, found to be upregulated in CRC. Finally, TMEM131 and DARS genes were identified in this study whose roles have never been interrogated in any kind of cancer, neither as a biomarker nor curative target. All the mentioned mechanisms must be further validated by experimental wet-lab techniques.

microRNAs (miRNAs) are negative regulators in a variety of cellular processes that occur in endometriosis. Therefore, functional polymorphisms in miRNA and miRNA binding sites may affect gene expression and contribute to susceptibility of endometriosis. In this study, we evaluated the association of two miRNA related polymorphisms, mir-126 rs4636297 and TGFβRI rs334348, with endometriosis risk and its severity. This case-control study was done on 157 endometriosis patients and 252 healthy women as a control group. Tetra amplification refractory mutation system-polymerase chain reaction (tetra-ARMS PCR) was designed to determine the polymorphisms. Our finding showed significant differences in genotype frequency of mir-126 rs4636297 between the groups (χ = 6.26, p = 0.044). A significant protection against endometriosis was found for mir-126 rs4636297 in allele (G versus A allele: OR = 0.695, 95% CI = 0.519-0.931, p = 0.015) and genotype (GG versus AA genotype: OR = 0.451, 95%CI = 0.233-0.873, p = 0.018). Significant association was also observed between the A allele and severity of endometriosis (OR = 0.478, 95%CI = 0.297-0.768, p = 0.002). Moreover, we found a significant association between AA genotype with the risk of endometriosis (OR = 0.493, 95%CI = 0.250-0.970, p = 0.041) and its severity (OR = 0.240, 95%CI = 0.065-0.883, p = 0.032) regarding TGFβRI rs334348 polymorphism. These finding suggest that, for the first time, mir-126 rs4636297 and TGFβRI rs334348 polymorphisms may influence individual's susceptibility to endometriosis and its severity.

Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.

Colorectal cancer is one of the leading causes of cancer death worldwide. Patient survival at the time of diagnosis depends largely on the stage of the tumor. Therefore, understanding the molecular mechanisms promoting cancer progression from early stages to high-grade stages is essential for therapeutic approaches. In the present study, we conducted transcriptomic data analysis employing a systems biology method to identify potential molecular targets for colorectal cancer treatment. These targets went under investigation one by one. We proposed some genes that their expression induction or suppression alone or in combination with each other would inhibit tumor progression or metastasis based on their biological activity. They are involved in cell proliferation, energy production under hypoxic conditions, epithelial to mesenchymal transition (EMT) and angiogenesis.Employing a network analysis viewpoint, some genes were discovered that has not been reported noticeably in any kind of cancer so far. As a result, they might have some roles in progression of colorectal cancer.

Worldwide prostate cancer (PCa) is recognized as the second most common diagnosed cancer and the fifth leading cause of cancer death among men globally. Rising incidence rates of PCa have been observed over the last few decades. It is necessary to improve prostate cancer detection, diagnosis, treatment and survival .However, there are few reliable biomarkers for early prostate cancer diagnosis and prognosis. In the current study, systems biology method was applied for transcriptomic data analysis to identify potential biomarkers for primary PCa.We firstly identified differentially expressed genes (DEGs) between primary PCa and normal samples. Then the DEGs were mapped in Wikipathways and gene ontology database to conduct functional categories enrichment analysis. 1575 unique DEGs with adjusted p-value < 0.05 were achieved from two sets of DEGs. 132 common DEGs between two sets of DEGs were retrieved. The final DEGs were selected from 60 common upregulated and 72 common downregulated genes between datasets. In conclusion, we demonstrated some potential biomarkers (FOXA1, AGR2, EPCAM, CLDN3, ERBB3, GDF15, FHL1, NPY, DPP4, and GADD45A) and HIST2H2BE as a candidate one which are tightly correlated with the pathogenesis of PCa.

Cellular redox homeostasis is the important tool for normal cell function and survival. Oxidants, reductants and antioxidants are the players to maintain cellular homeostasis balance. However, in some conditions like cancer, the concentration and activation of these players are disturbed.This study walks you through the molecular mechanism of redox homeostasis to describe how expression level of these players would help colorectal cancer (CRC) cells continue proliferation and survive in the hypoxic environment of tumor. We proposed that O2concentration is not detrimentally high in CRC cells since expression level of MnSOD didn't change noticeably. We also suggested that High proliferative CRC cells obtain their energy by oxidation of H2S in or Electron transport chain (ETC) and keep the adequate concentration of H2S by diminishing the expression level of enzymes involved in sulfide oxidation pathway. Reduction in hydrogen sulfide oxidation results in a decrease in the level of GSH. Glutathione peroxidase enzyme requires GSH to convert H2O2 into oxygen and water. Therefore, Level of hydrogen peroxide stays high which leads to an increase in cell proliferation. Furthermore, we analyzed the expression level of transcription factors sensitive to redox messengers. to cell proliferation while a severe increment and long-lasting in the concentration of these molecules causes cell death. As a result, if redox homeostasis is disturbed, oxidative stress contributes to aberrant cell growth/death and disease [2]. This happens by changes in cells environment and impaired antioxidants generation which modulate the concentration of oxidants [5]. ROS includes radical species such as superoxide (O2 -), hydroxyl radical ( . OH) and non-radical species like Hydrogen peroxide (H2O2). RNS involves nitric oxide (NO) and Peroxynitrite (ONOO -) [2, 6]. Moreover, there are two types of antioxidants, enzymatic and non-enzymatic (small molecules). SODs (Superoxide dismutase), Glutathione peroxidase (GPx) and Catalase are examples of enzymatic antioxidants but Glutathione (GSH), Thioredoxin (Tnx) and Peroxiredoxin (Prx) are examples of small molecule antioxidants. One of the primary ROS molecules is O2made in the ETC by transferring electrons from complex one and Three to a dioxygen molecule or by NAD(P)H oxidases (NOX) activation [7-10]. Superoxide is then converted into hydrogen peroxide using Superoxide dismutase enzymes [9]. Among the three kinds of SODs, SOD1 (CuZnSOD) is present in the cytoplasm, mitochondrial inter-membrane space, nucleus, and lysosomes while SOD2 (MnSOD) and SOD3 (Ec-SOD) are present in Mitochondria and Extra Cellular Matrix (ECM) respectively [2]. Next, H2O2 is turned into water and oxygen molecules by GPx enzyme which oxidizes reduced Glutathione (GSH) into oxidized glutathione (GSSG) [11]. GSSG is converted into GSH by Glutathione reductase (GR/GSR) and in the meantime, an NADPH is turned into NADP + . GSH can enter the oxidation cycle again and NADP + enters the glycolysis to be reduced into NADPH [12]. In the p...