Germ-line mutations of BRCA1 and BRCA2 genes are responsible for approximately 25-30% of dominantly inherited familial breast cancers; still a big part of genetic component is unknown. The aim of ...this study was to investigate genetic causes of familial breast cancer in a pedigree with recessive pattern of inheritance.
We applied exome sequencing as a useful approach in heterogeneous diseases gene identification in present study for familial breast cancer. Sanger sequencing was applied for validation and segregation analysis of mutations.
Here, we describe a family with three affected sisters of early-onset invasive ductal carcinoma due to heterozygous frame shift mutation rs80359352 in BRCA2 gene as the first report in Iranian patients in association with a novel missense SNP of STK11 (p.S422G). These mutations are inherited from their normal father.
Despite apparent recessive pattern of inheritance a dominant gene (here BRCA2) can be involved in pathogenesis of hereditary breast cancer which can be explained by incomplete penetrance of BRCA2 mutations.
Whole-exome sequencing (WES) has extensively been used in cancer genome studies; however, the use of WES data in the study of loss of heterozygosity or more generally allelic imbalance (AI) has so ...far been very limited, which highlights the need for user-friendly and flexible software that can handle low-quality datasets. We have developed a statistical approach, ExomeAI, for the detection of recurrent AI events using WES datasets, specifically where matched normal samples are not available.
ExomeAI is a web-based application, publicly available at: http://genomequebec.mcgill.ca/exomeai.
JavadNadaf@gmail.com or somayyeh.fahiminiya@mcgill.ca
Supplementary data are available at Bioinformatics online.
Whole-exome sequencing (WES) represents a significant breakthrough in the field of human genetics. This technology has largely contributed to the identification of new disease-causing genes and is ...now entering clinical laboratories. WES represents a powerful tool for diagnosis and could reduce the 'diagnostic odyssey' for many patients. In this review, we present a technical overview of WES analysis, variants annotation and interpretation in a clinical setting. We evaluate the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases. Finally, we discuss the efficacy of WES as a diagnostic tool and the impact on patient management.
Five main methods, commonly applied in genomic selection, were used to estimate the GEBV on the 15th QTLMAS workshop dataset: GBLUP, LASSO, Bayes A and two Bayes B type of methods (BBn and BBt). ...GBLUP is a mixed model approach where GEBV are obtained using a relationship matrix calculated from the SNP genotypes. The remaining methods are regression-based approaches where the SNP effects are first estimated and, then GEBV are calculated given the individuals' genotypes.
The differences between the regression-based methods are in their prior distributions for the SNP effects. The prior distribution for LASSO is a Laplace distribution, for Bayes A is a scaled Student-t distribution, and the Bayes B type methods have a Spike and Slab prior where only a proportion (π) of SNP has an effect, following a given distribution. In this study, two different distributions were considered for the Bayes B type methods: (i) normal and (ii) scaled Student-t. They are referred here as the BBn and BBt methods, respectively. These prior distributions are defined by one or more parameters controlling their scale/rate (λ), shape (df) or proportion of SNP with effect (π). LASSO requires one (λ); two for Bayes A (λ, df) and Bayes Bn (λ, π); and three for Bayes Bt (λ, df, π). In this study, all parameters were estimated from the data. An extra scenario for Bayes A and BBt was included where df was not estimated but fixed to 4 (suffixed _4df). The implementation of GBLUP was done using ASREML, the heritability was also estimated from the data. All other methods were implemented using a MCMC approach.
All Bayes A and B methods showed accuracy (correlation between True and Estimated BV) as high as 0.94 except for BA_4df (r = 0.91). Compared to the traditional BLUP using pedigree information, these methods improved the accuracy between 50 and 55%. GBLUP and LASSO were less accurate (0.81 and 0.85 respectively) and the improvements were 34 and 40% compared to BLUP.
Results of all methods were consistent and the accuracies for GEBV ranged between 0.81 and 0.94. When all parameters were estimated the results were similar for the Bayes A and Bayes B methods. Results showed that Bayes A was more sensitive to the changes in the shape parameter, and the parameter changes led to change in the accuracy of GEBV. However BBt was more robust to the change in this parameter. This may be explained by the fact that BBt estimates one extra parameter and it can buffer against a non-proper shape parameter.
Secreted protein, acidic, cysteine-rich (SPARC) is a glycoprotein that binds to collagen type I and other proteins in the extracellular matrix. Using whole-exome sequencing to identify the molecular ...defect in two unrelated girls with severe bone fragility and a clinical diagnosis of osteogenesis imperfecta type IV, we identified two homozygous variants in SPARC (GenBank: NM_003118.3; c.497G>A p.Arg166His in individual 1; c.787G>A p.Glu263Lys in individual 2). Published modeling and site-directed mutagenesis studies had previously shown that the residues substituted by these mutations form an intramolecular salt bridge in SPARC and are essential for the binding of SPARC to collagen type I. The amount of SPARC secreted by skin fibroblasts was reduced in individual 1 but appeared normal in individual 2. The migration of collagen type I alpha chains produced by these fibroblasts was mildly delayed on SDS-PAGE gel, suggesting some overmodification of collagen during triple helical formation. Pulse-chase experiments showed that collagen type I secretion was mildly delayed in skin fibroblasts from both individuals. Analysis of an iliac bone sample from individual 2 showed that trabecular bone was hypermineralized on the material level. In conclusion, these observations show that homozygous mutations in SPARC can give rise to severe bone fragility in humans.
Several moderate- and high-risk breast cancer susceptibility genes have been discovered, but more are likely to exist. To discover new breast cancer susceptibility genes, we used 2 populations (from ...Poland and Quebec, Canada) and applied whole-exome sequencing in a discovery phase (n = 195), followed by validation. We identified rare recurrent RECQL mutations in each population. In Quebec, 7 of 1,013 higher-risk breast cancer cases and 1 of 7,136 newborns carried the c.634C>T (p.Arg215*) variant (P = 0.00004). In Poland, 30 of 13,136 unselected breast cancer cases and 2 of 4,702 controls carried the c.1667_1667+3delAGTA (p.K555delinsMYKLIHYSFR) variant (P = 0.008). RECQL is implicated in resolving stalled DNA replication forks to prevent double-stranded DNA (dsDNA) breaks. This function is related to that of other known breast cancer susceptibility genes, many of which are involved in repairing dsDNA breaks. We conclude that RECQL is a breast cancer susceptibility gene.
To date, epimutations reported in man have been somatic and erased in germlines. Here, we identify a cause of the autosomal recessive cblC class of inborn errors of vitamin B
metabolism that we name ..."epi-cblC". The subjects are compound heterozygotes for a genetic mutation and for a promoter epimutation, detected in blood, fibroblasts, and sperm, at the MMACHC locus; 5-azacytidine restores the expression of MMACHC in fibroblasts. MMACHC is flanked by CCDC163P and PRDX1, which are in the opposite orientation. The epimutation is present in three generations and results from PRDX1 mutations that force antisense transcription of MMACHC thereby possibly generating a H3K36me3 mark. The silencing of PRDX1 transcription leads to partial hypomethylation of the epiallele and restores the expression of MMACHC. This example of epi-cblC demonstrates the need to search for compound epigenetic-genetic heterozygosity in patients with typical disease manifestation and genetic heterozygosity in disease-causing genes located in other gene trios.
Abstract
Background
Glioblastoma is a treatment-resistant brain cancer. Its hierarchical cellular nature and its tumor microenvironment (TME) before, during, and after treatments remain unresolved.
...Methods
Here, we used single-cell RNA sequencing to analyze new and recurrent glioblastoma and the nearby subventricular zone (SVZ).
Results
We found 4 glioblastoma neural lineages are present in new and recurrent glioblastoma with an enrichment of the cancer mesenchymal lineage, immune cells, and reactive astrocytes in early recurrences. Cancer lineages were hierarchically organized around cycling oligodendrocytic and astrocytic progenitors that are transcriptomically similar but distinct to SVZ neural stem cells (NSCs). Furthermore, NSCs from the SVZ of patients with glioblastoma harbored glioblastoma chromosomal anomalies. Lastly, mesenchymal cancer cells and TME reactive astrocytes shared similar gene signatures which were induced by radiotherapy in a myeloid-dependent fashion in vivo.
Conclusion
These data reveal the dynamic, immune-dependent nature of glioblastoma’s response to treatments and identify distant NSCs as likely cells of origin.
Abstract
Post-craniotomy recovery in a neuro-critical care unit (NCCU) has been routine for most patients. There is no evidence to support this practice. To address this, we assessed the development ...of post-operative adverse events in brain tumor resection patients surveilled in the NCCU or the post-anesthesia care unit (PACU).
METHODS: All brain tumor craniotomies performed between 2016-2021 (KP) were reviewed. Inclusion criteria were: age >18; craniotomy for biopsy or resection of intracerebral or extracerebral tumors. Cohorts were divided into two groups based on recovery destination: NCCU or PACU. Past medical history, pre- and post-operative neuroradiological imaging, surgical resection features, and neuropathology results were reviewed for both groups. RESULTS: There were 681 patients in NCCU group and 397 in the PACU group. Mean ages were 55.6 (NCCU) and 59.7 (PACU) (p <0.001). The American Society of Anesthesiologists (ASA) class was not significantly different between groups (p=0.89). Median recovery time in the NCCU group was 19 hours, and 4 hours in the PACU group. The incidence of adverse events within 24 hours post- surgery was 0.04 in NCCU group and 0.03 in PACU group (p=0.46). Post-operative hospital stay was 9.5 days in the NCCU group and 8.5 days in PACU group (p <0.001). CONCLUSION: The incidence of adverse events within 24 hours post brain tumor surgery is not different between patients being surveilled for a long period in a NCCU, or a short period in a PACU.
Abstract
Background
Sixty percent of surgically resected brain metastases (BrM) recur within 1 year. These recurrences have long been thought to result from the dispersion of cancer cells during ...surgery. We tested the alternative hypothesis that invasion of cancer cells into the adjacent brain plays a significant role in local recurrence and shortened overall survival.
Methods
We determined the invasion pattern of 164 surgically resected BrM and correlated with local recurrence and overall survival. We performed single-cell RNA sequencing (scRNAseq) of >15,000 cells from BrM and adjacent brain tissue. Validation of targets was performed with a novel cohort of BrM patient-derived xenografts (PDX) and patient tissues.
Results
We demonstrate that invasion of metastatic cancer cells into the adjacent brain is associated with local recurrence and shortened overall survival. scRNAseq of paired tumor and adjacent brain samples confirmed the existence of invasive cancer cells in the tumor-adjacent brain. Analysis of these cells identified cold-inducible RNA-binding protein (CIRBP) overexpression in invasive cancer cells compared to cancer cells located within the metastases. Applying PDX models that recapitulate the invasion pattern observed in patients, we show that CIRBP is overexpressed in highly invasive BrM and is required for efficient invasive growth in the brain.
Conclusions
These data demonstrate peritumoral invasion as a driver of treatment failure in BrM that is functionally mediated by CIRBP. These findings improve our understanding of the biology underlying postoperative treatment failure and lay the groundwork for rational clinical trial development based upon invasion pattern in surgically resected BrM.
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