Page 10 - TD-3-1

Tumor Discovery Haplotype and LD of BRCA genes in GBM

machineries, USA). Thereafter, using the Ion Torrent PGM 3. Results
platform (Ion Torrent PGM, Life Machineries, USA), all
barcode-enriched samples were sequenced using the Ion 3.1. Clinical characteristics of the recruited
318 Chip Kit V2 BC (Life Technologies Ltd., USA). The individuals
depth of analysis was considered to be at least ×500. A total of 44 individuals were sequenced for BRCA
mutations, and they were categorized according to their
2.7. Files examination diagnosis into 15 GBM patients and 29 healthy normal
The annotations for the variations in the BRCA1 individuals as controls. Both the GBM and control groups
and BRCA2 genes were carried out using the cloud- were the same age, as there was no significant difference
constructed IonReporter Outfit software (version 5.4.0, between their ages. In terms of gender status, there were
Life machineries). The annotations were subsequently ten females and five males in GBM, while there were
associated with human genome hg19 (Genome 17 females and 12 males in controls.
Reference Consortium GRCh37) through the Ion According to the ECGO system, GBM patients were
Torrent Server and different caller plugins, according divided into two groups: those above two (9 cases, 60%)
to the criteria mentioned for the BRCA1 and BRCA2
panels. Investigation of alternatives was practical without and those below or equal to two (6 cases, 40%). The
prejudice, and the position arrangements for BRCA1 sites of the primary lesion were frontal (n = 6), temporal
and BRCA2 were NM_007300.3 and NM_000059.3, (n = 5), and occipital (n = 4). Nine of the GBM patients
respectively. who received surgical treatment underwent a biopsy, and
the remaining six underwent either a total or sub-total
Haplotype analysis is the determination of the pattern excision. Then, ten GBM patients received radiotherapy/
of adjacent SNPs on the matching chromosome and chemotherapy for six cycles, and three patients received
heritability in a unit. Units may comprise a huge number the same treatment for three cycles, while the remaining
of SNPs, but limited SNPs are sufficient to exclusively patients received only radiotherapy. The GBM patients
recognize the haplotypes in units. The HapMap is a chart responded to the treatment strategies as follows: three
of these haplotype units, and the exact SNPs that classify GBM patients reported a CR, six GBM patients reported a
the haplotypes are called tag SNPs. PR, two showed SD, and the remaining four reported PD.
Linkage disequilibrium – the non-random connection The demographic and medical criteria are summarized in
of alleles at altered loci – is a sympathetic marker of the Table 1.
population-inherited forces that establish a genome. Due
to the tremendous progress in approaches for measuring 3.2. Haplotype analysis for BRCA gene mutations
genetic differences at a fine scale, evolutionary biologists In our previous study, six GBM patients were sequenced
and human geneticists are progressively exploiting for the detection of BRCA gene mutations, and the
17
linkage disequilibrium to recognize past evolutionary authors accordingly reported 13 single-nucleotide
and demographic measures, to map genes that are linked variations (SNVs) for the BRCA1 gene using the LD matrix
with measurable personalities and heritable illnesses, and of the LDlink tool. Seven of these SNPs showed strong LD.
to recognize the shared development of related groups of Accordingly, these SNPs were separated into haplotype-like
genes. LDlink (https://ldlink.nci.nih.gov/?tab=ldmatrix) designs, and the LD matrix of the LDlink tool was used to
is a set of web-based appliances to easily and proficiently investigate whether there was LD between the investigated
interrogate LD in populations, with flexible query and SNPs compared to all data populations.
communicative visualization of results.
In the present study, we have sequenced BRCA genes
The haplotype tables and communicating plots in a total of 44 individuals, with 15 identified as GBM
generated by LDlink are tailored for researchers interested cases and the remaining as healthy controls. The primary
in mapping common and rare disease susceptibility objective was to investigate haplotype frequency in GBM
loci, with an emphasis on linking associated alleles and cases compared to the recruited healthy individuals and to
highlighting potentially functional variants. compare our findings with the data population. Accordingly,
In the present study, for the comprehensive investigation haplotype analysis and frequency assessments were carried
of LD and haplotype, the identified variations in both out for the reported seven SNPs using the LDhap tool
BRCA1 and BRCA2 were analyzed using the LDlink for all populations. Of these SNPs, five haplotypes were
application. This is in contradiction to all population previously reported among the data population, four of
records, as there is currently no detailed Egyptian them were frequently reported, one was rare, and three
population database accessible. haplotypes were newly reported, as shown in Table 2.

Volume 3 Issue 1 (2024) 4 https://doi.org/10.36922/td.1480