arrays CGH

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

Background: DiGeorge syndrome (DGS), caused by a deletion del(22)(q11.2q11.2), is the most frequently observed microdeletion syndrome. There is a vast clinical heterogeneity in DGS, and several studies suggested also heterogeneity of clinical signs and phenotypic appearance to be related to ethnic differences. Here, clinical characteristics of 72 patients with molecular diagnosed deletion del(22)(q11.2q11.2) derived from different countries from Europe, America, Africa, and Asia are summarized and compared. Results: Unless ethnic differences, the expected major clinical signs were present in all cases. Frequent clinical manifestations found in this study were congenital heart disease with 68% (49/72), followed by dysmorphic features found in 61% (44/72); neurodevelopmental disorders were present in 43% (31/72) and thymus hypoplasia/aplasia in 32% (23/72). However, clinical features of the patients appeared/were recognized at different times during their lives. Within the group, under 2 years predominated heart disease, dysmorphic features, and hypocalcemia and/or hypoparathyroidism. In the group older than 2 years, the following combination of clinical findings was most frequent: dysmorphic features, congenital heart disease, intellectual disability, and immunological disorders. In the eight cases detected prenatally, abnormal sonographic findings were the major clinical signs (cardiovascular malformations and renal malformations). Conclusions: Despite the heterogeneous nature of the sample analyzed, a number of clinical findings could be highlighted to be useful for the clinical delineation of this DGS. Interestingly, diagnostic indicators may vary depending on the age at diagnosis. Finally, apparent differences in DGS patients from different regions seem to be rather due to applied test systems than to real differences in patients from different ethnicities.

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

Genomic instability contributes to the neoplastic phenotype by deregulating key cancer-related genes, which in turn can have a detrimental effect on patient outcome. DNA amplification of the 8p11-p12 genomic region has clinical and biological implications in multiple malignancies, including breast carcinoma where the amplicon has been associated with tumor progression and poor prognosis. However, oncogenes driving increased cancer-related death and recurrent genetic features associated with the 8p11-p12 amplicon remain to be identified. In this study, DNA copy number and transcriptome profiling data for 229 primary invasive breast carcinomas (corresponding to 185 patients) were evaluated in conjunction with clinicopathological features to identify putative oncogenes in 8p11-p12 amplified samples. Illumina paired-end whole transcriptome sequencing and whole-genome SNP genotyping were subsequently performed on 23 samples showing high-level regional 8p11-p12 amplification to characteri...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

Breast cancer brain metastases remain a significant clinical problem. Chemotherapy is ineffective and a lack of treatment options result in poor patient outcomes. Targeted therapeutics have proven to be highly effective in primary breast cancer, but lack of molecular genomic characterization of metastatic brain tumors is hindering the development of new treatment regimens. Here we contribute to fill this void by reporting on gene copy number variation (CNV) in 10 breast cancer metastatic brain tumors, assayed by array comparative genomic hybridization (aCGH). Results were compared to a list of cancer genes verified by others to influence cancer. Cancer gene aberrations were identified in all specimens and pathway-level analysis was applied to aggregate data, which identified stem cell pluripotency pathway enrichment and highlighted recurring, significant amplification of SOX2, PIK3CA, NTRK1, GNAS, CTNNB1, and FGFR1. For a subset of the metastatic brain tumor samples (n = 4) we compa...

Recently, one discretization of a continuous distribution, the socalled discrete transmuted generalized inverse Weibull (DTGIW) distribution, has been suggested. In this article, we propose the application of the DTGIW distribution along with using the dtgiw package in the R language program to be analyzed the discretized data or count data. We estimate the model parameters by using the maximum likelihood (ML), Anderson-Darling (AD), and least-square (LS) methods. We compare the performances of the proposed estimators based on numerical calculations for various values of the distribution parameters, and sample sizes in terms of the root mean squared error and estimated values. Simulation results show that the ML method is most efficient for a large sample size. We analyze two applications to illustrate the applicability of the DTGIW distribution with the results showing that the DTGIW distribution is an alternative flexible in analyzing these count data.

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

Breast cancer (BC) in Nigeria is characterized by disproportionately aggressive molecular subtypes. C-reactive protein (CRP) is associated with risk and aggressiveness for several types of cancer. We examined the association of high-sensitivity CRP (hsCRP) with odds of BC by molecular subtype among Nigerian women. Among 296 newly diagnosed BC cases and 259 healthy controls, multivariable logistic regression models were used to estimate adjusted odds ratios (aOR) and 95% confidence intervals (CI) for the association between hsCRP and odds of BC overall and by molecular subtype (luminal A, luminal B, HER2-enriched and triple-negative or TNBC). High hsCRP (> 3 mg/L) was observed in 57% of cases and 31% of controls and was associated with 4 times the odds of BC (aOR: 4.43; 95% CI: 2.56, 7.66) after adjusting for socio-demographic, reproductive, and clinical variables. This association persisted regardless of menopausal status and body mass index (BMI) category. High hsCRP was associa...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

Since the approval of the first poly (adenosine diphosphate [ADP]) ribose polymerase inhibitor (PARPi; olaparib [Lynparza™]) for platinum-sensitive relapsed high grade ovarian cancer, with either germline or somatic deleterious variants, the strategies for are dynamically changing. Along with germline testing within the context of familial or sporadic ovarian cancer, patients are now being referred for genetic assay above all for treatment decisions: in this setting tumour BRCA assay can allow to identify an estimated 3-9% of patients with peculiar somatic mutations. These women could also benefit from PARPi therapy. This new type of approach is really challenging, in particular due to the technical and analytical difficulties regarding low quality DNA deriving from formalin-fixed, paraffin-embedded (FFPE) specimens. in this manuscript, we try to a) underline many issues related to analysis by next generation sequencing technologies (NGS), b) provide some responses to many questions...

Following the publication of the first human genome, OMICs research, including genomics, transcriptomics, proteomics, and metagenomics, has been on the rise. OMICs studies revealed the complex genetic diversity among human populations and challenged our understandings of genotype-phenotype correlations. Africa, being the cradle of the first modern humans, is distinguished by a large genetic diversity within its populations and rich ethnolinguistic history. However, the available human OMICs tools and databases are not representative of this diversity, therefore creating significant gaps in biomedical research. African scientists, students, and publics are among the key contributors to OMICs systems science. This expert review examines the pressing issues in human OMICs research, education, and development in Africa, as seen through a lens of computational biology, public health relevant technology innovation, critically-informed science governance, and how best to harness OMICs data to benefit health and societies in Africa and beyond. We underscore the disparities between North and Sub-Saharan Africa at different levels. A harmonized African ethnolinguistic classification would help address annotation challenges associated with population diversity. Finally, building on the existing strategic research initiatives, such as the H3Africa and H3ABioNet Consortia, we highly recommend addressing large-scale multidisciplinary research challenges, strengthening research collaborations and knowledge transfer, and enhancing the ability of African researchers to influence and shape national and international research, policy, and funding agendas. This article and analysis contribute to a deeper understanding of past and current challenges in the African OMICs innovation ecosystem, while also offering foresight on future innovation trajectories.

The application of genomics technologies to medicine and biomedical research is increasing in popularity, made possible by new high-throughput genotyping and sequencing technologies and improved data analysis capabilities. Some of the greatest genetic diversity among humans, animals, plants and microbiota occurs in Africa, yet genomic research outputs from the continent are limited. The H3Africa initiative was established to drive the development of genomic research for human health in Africa and through recognition of the critical role of bioinformatics in this process, spurred the establishment of H3ABioNet, a pan-African Bioinformatics network for H3Africa. The limitations in bioinformatics capacity on the continent have been a major contributory factor to the lack of notable outputs in high-throughput biology research. While pockets of high quality bioinformatics teams have existed previously, the majority of research institutions lack experienced faculty who can train and super...

ABSTRACT Background: About 5-10% of breast/ovarian cancers are hereditary. However, for a large proportion of cases (around 50%), the genetic cause remains unknown. These cases are grouped in a separated BRCAX category. The aim of this study was to identify genomic alterations in BRCA1/BRCA2 wild-type tumor samples from women with family history strongly suggestive of hereditary breast/ovarian cancer. Results: A cohort of 31 Brazilian women was included in the study. Using the GISTIC algorithm, we identified 20 regions with genomic gains and 31 with losses. The most frequent altered regions were 1q21.2, 6p22.1 and 8p23.3 in breast tumors and Xq26 and Xp22.32-22.31 among the ovarian cancer cases. An interesting association identified was the loss of 22q13.31-13.32 and the presence of ovarian cancer cases. Among the genes present in the frequently altered regions, we found FGFR1, NSMCE2, CTTN, CRLF2, ERBB2, STARD3, MIR3201 and several genes of RAET and ULBP family. Conclusions: In conclusion, our results suggest that alterations on chromosomes 1, 6, 8 and X are common on BRCAX tumors and that the loss on 22q can be associated with the presence of ovarian cancer. Methods: DNA copy number alterations were analyzed by 60K array comparative genomic hybridization in breast and ovarian FFPE tumors.

Knowledge management is a key element in medical environments. Arrays CGH make possible the realization of tests on patients for the detection of mutations in chromosomal regions. The detection of the regions with mutations associated to different pathologies is an important step for the selection of relevant genes, proteins or diseases. The corresponding information of the mutations and genes is distributed in different public sources and databases, so it is necessary the use of systems that allow to contrast different sources for the selection of outstanding information. In this work, a case-based reasoning (CBR) system is presented to carry out the automatic selection of relevant segments and the associated genes or proteins that could determine different pathologies. The CBR system integrates statistical techniques for the selection of relevant genes and visualization techniques for the interpretation of the final results.