Background: Large rearrangements account for 8% to 15% of deleterious BRCA mutations, although none have been characterized previously in individuals of Mexican ancestry.
Methods: DNA from 106 ...Hispanic patients without an identifiable BRCA mutation by exonic sequence analysis was subjected to multiplexed quantitative differential PCR. One case of Native American
and African American ancestry was identified via multiplex ligation-dependent probe amplification. Long-range PCR was used
to confirm deletion events and to clone and sequence genomic breakpoints. Splicing patterns were derived by sequencing cDNA
from reverse transcription-PCR of lymphoblastoid cell line RNA. Haplotype analysis was conducted for recurrent mutations.
Results: The same deletion of BRCA1 exons 9 through 12 was identified in five unrelated families. Long-range PCR and sequencing indicated a deletion event of
14.7 kb. A 3-primer PCR assay was designed based on the deletion breakpoints, identified within an Alu Sp element in intron 8 and an Alu Sx element in intron 12. Haplotype analysis confirmed common ancestry. Analysis of cDNA showed direct splicing of exons 8
to 13, resulting in a frameshift mutation and predicted truncation of the BRCA1 protein.
Conclusions: We identified and characterized a novel large BRCA1 deletion in five unrelated families—four of Mexican ancestry and one of African and Native American ancestry, suggesting
the possibility of founder effect of Amerindian or Mestizo origin. This BRCA1 rearrangement was detected in 3.8% (4 of 106) of BRCA sequence-negative Hispanic families. An assay for this mutation should be considered for sequence-negative high-risk Hispanic
patients. (Cancer Epidemiol Biomarkers Prev 2007;16(8):1615–20)
Classification of rare missense variants as neutral or disease causing is a challenge and has important implications for genetic counseling. A multifactorial likelihood model for classification of ...unclassified variants in BRCA1 and BRCA2 has previously been developed, which uses data on co-occurrence of the unclassified variant with pathogenic mutations in the same gene, cosegregation of the unclassified variant with affected status, and Grantham analysis of the fit between the missense substitution and the evolutionary range of variation observed at its position in the protein. We have further developed this model to take into account relevant features of BRCA1- and BRCA2-associated tumors, such as the characteristic histopathology and immunochemical profiles associated with pathogenic mutations in BRCA1, and the fact that approximately 80% of tumors from BRCA1 and BRCA2 carriers undergo inactivation of the wild-type allele by loss of heterozygosity. We examined 10 BRCA1 and 15 BRCA2 unclassified variants identified in Australian, multiple-case breast cancer families. By a combination of genetic, in silico, and histopathologic analyses, we were able to classify one BRCA1 variant as pathogenic and six BRCA1 and seven BRCA2 variants as neutral. Five of these neutral variants were also found in at least 1 of 180 healthy controls, suggesting that screening a large number of appropriate controls might be a useful adjunct to other methods for evaluation of unclassified variants.
: Victim identification initiatives undertaken in the wake of Mass Fatality Incidents (MFIs) where high‐body fragmentation has been sustained are often dependent on DNA typing technologies to ...complete their mandate. The success of these endeavors is linked to the choice of DNA typing methods and the bioinformatic tools required to make the necessary associations. Several bioinformatic tools were developed to assist with the identification of the victims of the World Trade Center attacks, one of the most complex incidents to date. This report describes one of these tools, the Mass Disaster Kinship Analysis Program (MDKAP), a pair‐wise comparison software designed to handle large numbers of complete or partial Short Tandem Repeats (STR) genotypes, and infer identity of, or biological relationships between tested samples. The software performs all functions required to take full advantage of the information content of processed genotypic data sets from large‐scale MFIs, including the collapse of victims data sets, remains re‐association, virtual genotype generation through gap‐filling, parentage trio searching, and a consistency check of reported/inferred biological relationships within families. Although very few WTC victims were genetically related, the software can detect parentage trios from within a victim’s genotype data set through a nontriangulated approach that screens all possible parentage trios. All software‐inferred relationships from WTC data were confirmed by independent statistical analysis. With a 13 STR loci complement, a fortuitous parentage trio (FPT) involving nonrelated individuals was detected. Additional STR loci would be required to reduce the risk of an FPT going undetected in large‐scale MFIs involving related individuals among the victims. Kinship analysis has proven successful in this incident but its continued success in larger scale MFIs is contingent on the use of a sufficient number of STR loci to reduce the risk of undetected FPTs, the use of mtDNA and Y‐STRs to confirm parentage and of bioinformatics that can support large‐scale comparative genotyping schemes capable of detecting parentage trios from within a group of related victims.
During the last 10 years, the introduction of PCR-based DNA typing technologies in forensic applications has been highly successful. This technology has become pervasive throughout forensic ...laboratories and it continues to grow in prevalence. For many criminal cases, it provides the most probative evidence. Criminal genotype data banking and victim identification initiatives that follow mass-fatality incidents have benefited the most from the introduction of automation for sample processing and data analysis. Attributes of offender specimens including large numbers, high quality and identical collection and processing are ideal for the application of laboratory automation. The magnitude of kinship analysis required by mass-fatality incidents necessitates the application of computing solutions to automate the task. More recently, the development activities of many forensic laboratories are focused on leveraging experience from these two applications to casework sample processing. The trend toward increased prevalence of forensic genetic analysis will continue to drive additional innovations in high-throughput laboratory automation and information systems.
The economy and the banking business have experienced drastic changes in the last few years. To make matters worse, the financial world is facing volumes of new regulations while the media and ...elected officials have had a field day beating up on financial institutions. Last month Gallup.com reported that Americans' confidence in U.S. banks remains near its all-time low at 23% - essentially unchanged from 22% last year, and far below the 41% prerecession level of June 2007. This article discusses the concerns and worries of financial CEOs and other bank managers.
There is a thread running through the more successful community banks. The president takes an active role in marketing. That means the president must be the bank's strongest advocate of its brand ...position. If you are not sure what your brand position is, then you need to be an advocate of researching the market and developing a strategic plan for branding your bank. Once the brand is in place, the president needs to be its strongest promoter.
CTS Advertising conducted an informal survey of community banks, asking the bank leaders and business people who work with them to comment on the most important marketing challenges that community ...banks face today. Tom Van Buren, president at West Shore Bank (Scottville, Michigan) said the toughest marketing challenge for many community banks is developing a market plan that includes branches in many different communities with a wide diversity in both economic and social cultures. Today, community banks absolutely must pay attention to marketing. Banks should recognize that their marketing wars can no longer be won with a free calendar or small space rate ads.
Organoids generated from human pluripotent stem cells provide experimental systems to study development and disease, but quantitative measurements across different spatial scales and molecular ...modalities are lacking. In this study, we generated multiplexed protein maps over a retinal organoid time course and primary adult human retinal tissue. We developed a toolkit to visualize progenitor and neuron location, the spatial arrangements of extracellular and subcellular components and global patterning in each organoid and primary tissue. In addition, we generated a single-cell transcriptome and chromatin accessibility timecourse dataset and inferred a gene regulatory network underlying organoid development. We integrated genomic data with spatially segmented nuclei into a multimodal atlas to explore organoid patterning and retinal ganglion cell (RGC) spatial neighborhoods, highlighting pathways involved in RGC cell death and showing that mosaic genetic perturbations in retinal organoids provide insight into cell fate regulation.
•A novel stability analysis has been developed for partitioned CHT methods.•A new partitioned coupling method is presented with enhanced stability.•Stability analysis is extensively validated on flat ...plate test case.•A stable method to compute the numerical Biot number is proposed.•The influence of the type of boundary conditions on stability is explained.
The prediction of the heat transfer between a fluid and a solid object, known as conjugate heat transfer, is a very common problem in engineering sciences. This work investigates coupling methods which allow to solve such problems numerically by using separate solvers for both domains. The methods converge to the conjugate solution by exchanging boundary conditions at their interface. We review three known methods while postulating a forth novel method with improved stability properties.
Even though this coupling methods use standard solvers for each domain with known stability properties, many reports in the literature are found on instabilities occurring during the coupling procedure. While it is known that the origin of this problem lies at the exchange of boundary conditions, to date no closing stability criterion could be found.
The present work aims to provide a quantitative answer as to why these instabilities occur and to provide guidelines with respect to the use of the different methods. A new stability criterion is derived based on several simplifications. It shows that each method has its own stability limit and can be used within a specific range of applications, mainly dominated by the Biot number. Although the criterion is derived by making strong assumptions, it is validated through series of numerical experiments on a flat plate test case. It shows that we have correctly identified the mechanism leading to instabilities.
Finally, we compare the novel coupling strategy with the established methods. Considering the stability the new approach is advantageous especially for high Biot numbers, concluding that it can improve efficiency and accuracy of conjugate heat transfer computations.
