Question

1-What determines the detection resolution of a given DNA microarray?

2-What does c.1353C>T mean?

Answer 1

Answer :1

Viruses transmitted by small mammals and arthropods serve as global threats to humans. Most emergent and re-emergent viral agents are transmitted by these groups; therefore, the development of high-throughput screening methods for the detection and surveillance of such viruses is of great interest. In this study, we describe a DNA microarray platform that can be used for screening all viruses transmitted by small mammals and arthropods (SMAvirusChip) with nucleotide sequences that have been deposited in the GenBank. SMAvirusChip was designed with more than 15,000 oligonucleotide probes (60-mers), including viral and control probes. Two SMAvirusChip versions were designed: SMAvirusChip v1 contains 4209 viral probes for the detection of 409 viruses, while SMAvirusChip v2 contains 4943 probes for the detection of 416 viruses. SMAvirusChip was evaluated with 20 laboratory reference-strain viruses. These viruses could be specifically detected when alone in a sample or when artificially mixed within a single sample. The sensitivity of SMAvirusChip was evaluated using 10-fold serial dilutions of dengue virus (DENV). The results showed a detection limit as low as 2.6E3 RNA copies/mL. Additionally, the sensitivity was one log10 lower (2.6E2 RNA copies/mL) than quantitative real-time RT-PCR and sufficient to detect viral genomes in clinical samples. The detection of DENV in serum samples of DENV-infected patients (n = 6) and in a whole blood sample spiked with DENV confirmed the applicability of SMAvirusChip for the detection of viruses in clinical samples. In addition, in a pool of mosquito samples spiked with DENV, the virus was also detectable. SMAvirusChip was able to specifically detect viruses in cell cultures, serum samples, total blood samples and a pool of mosquitoes, confirming that cellular RNA/DNA did not interfere with the assay. Therefore, SMAvirusChip may represent an innovative surveillance method for the rapid identification of viruses transmitted by small mammals and arthropods.

DNA microarrays can be used to detect DNA (as in comparative genomic hybridization), or detect RNA (most commonly as cDNA after reverse transcription) that may or may not be translated into proteins. The process of measuring gene expression via cDNA is called expression analysis or expression profiling.

Since their development in the mid-1990s, DNA microarrays have become a key tool in the fight against cancer. ... For instance, microarrays are currently a key tool in genetic diagnosis, allowing doctors to identify specific subtypes within an overall disease category based on differences in gene expression.

Answer :2

Germline mutations in tumour suppressor genes BRCA1 and BRCA2 confer susceptibility to breast and ovarian cancers. We previously reported BRCA1 mutations and sequence variants in a group of Sri Lankan breast cancer patients. Here we report for the first time mutations and sequence variants of BRCA2 using the same cohort. A total of 120 patients with (N=70) and without (N=50) a family history of breast cancer and 20 healthy controls were studied. Twelve exons (exons 2, 5, 6, 7, 9, 17, 23 in familial and sporadic cases; exons 3, 10, 19, 22, 27 in familial cases) were screened by Single Strand Conformation Polymorphism (SSCP). All the samples showing abnormal bands on SSCP and representative samples from those not showing abnormal bands were directly sequenced. Ten sequence variants were found in exons 2, 9 and 10. One reported sequence variant: c.203G>A/exon2 (44 familial and 39 sporadic cases), one novel silent mutation: c.969C>T/exon9, one novel missense mutation: c.971C>G/exon9, and one reported intronic variant: IVS8-1G>C/exon9 (in one familial case each) were detected. In exon 10, three reported missense mutations: c.1093A>C (10 familial cases), c.1342A>T/C (58 familial cases) and c.1352C>T (4 familial cases), one novel missense mutation: c.1191A>C (5 familial cases), one novel silent mutation: c.1353C>T (1 familial case) and one reported silent mutation: c.1593A>G (5 familial cases) were characterized. We have found six previously reported sequence variants and four novel mutations of BRCA2 gene in this cohort of patients. Studies are in progress to screen the remaining exons of BRCA2 gene.