• Asian Pacific Journal of Cancer Prevention
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• v.13 no.7
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• pp.3349-3355
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• 2012

Background and objectives: Chromosomal abnormalities play an important role in genesis of acute lymphoblastic leukemia (ALL) and have prognostic implications. Five major risk stratifying fusion genes in ALL are BCR-ABL, MLL-AF4, ETV6-RUNX11, E2A-PBX1 and SIL-TAL1. This work aimed to detect common chromosomal translocations and associated fusion oncogenes in adult ALL patients and study their relationship with clinical features and treatment outcome. Methods: We studied fusion oncogenes in 104 adult ALL patients using RT-PCR and interphase-FISH at diagnosis and their association with clinical characteristics and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL (t 9; 22), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (Del 1p32) were found in 82/104 (79%) patients. TCF3-PBX1 fusion gene was associated with lymphadenopathy, SIL-TAL1 positive patients had frequent organomegaly and usually presented with a platelets count of less than $50{\times}10^9/l$. Survival of patients with fusion gene ETV6-RUNX1 was better when compared to patients harboring other genes. MLL-AF4 and BCR-ABL positivity characterized a subset of adult ALL patients with aggressive clinical behaviour and a poor outcome. Conclusions: This is the first study from Pakistan which investigated the frequency of5 fusion oncogenes in adult ALL patients, and their association with clinical features, treatment response and outcome. Frequencies of some of the oncogenes were different from those reported elsewhere and they appear to be associated with distinct clinical characteristics and treatment outcome. This information will help in the prognostic stratification and risk adapted management of adult ALL patients.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.43-45
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• 2013

Background: The aim of this epidemiological study was to establish the laterality of breast cancer (BC) and its association with size, receptor status of the primary tumor and bone metastasis (BM) in a local population. Materials and Methods: This retrospective study included cases of BC from Jan-2009 to Dec-2011 who were referred for metastatic work up or follow up survey with Technetium-99m MDP bone scan (BS) to the Nuclear Medicine Department of Karachi Institute of Radiotherapy and Nuclear Medicine (KIRAN). A total of 384 patients out of 521 were included and all reviewed for age, primary tumor size (PTS), laterality, receptor status like estrogen receptor (ER) progesterone receptor (PR) and Her-2-Neu receptor, presence or absence of BM with sites of involvement and time interval between diagnosis of BC and appearance of BM. Results: The left to right sided BC proportion was significantly higher than unity (59%:41%; p<0.001). The right sided BC was observed in younger age group (46:52 years; p<0.0001) and with a smaller PTS than the left sided (3.43:4.15 cm; p<0.0001). The patients with BM had relatively higher negative receptor status with a significant predominance of right sided BC. The overall incidence of BM on BS was 28% and relatively higher in right than left breast (33%:24% p=0.068). The average number of BM sites was also significantly greater for the right side (6:4, P<0.0001). The % cumulative risk of BM in right breast was noted at significantly smaller PTS than left side with log rank value of 5.579; p<0.05. The Kaplan Meier survival plot for event free survival of BM in left sided BC was significantly higher than for the right side (log rank value=4.155, p<0.05), with an earlier appearance of BM in right BC. Conclusions: 1) A left sided predominance of BC was seen in local population; 2) right sided BC had a more aggressive behavior with extensive and earlier appearance of BM at relatively younger age, smaller PTS and receptor (s) negativity.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.7
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• pp.4353-4358
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• 2013

Introduction: Breast cancer aggressiveness can be correlated with proliferation status of tumor cells, which can be ascertained with tumor grade and Ki67 indexing. However due to lack of reproducibility, the ASCO do not recommend routine use of Ki67 in determining prognosis in newly diagnosed breast cancers. We therefore aimed to determine associations of the Ki67 index with other prognostic markers like tumor size, grade, lymph node metastasis, ER, PR and HER2neu status. Methods: A total of 194 cases of newly diagnosed breast cancer were included in the study. Immunohistochemical staining for ER, PR, HER2neu and Ki67 was performed by the DAKO envision method. Associations of the Ki67 index with other prognostic factors were evaluated both as continuous and categorical variables. Results: Mean age of the patients was 51.7 years (24-90). Mean Ki67 index was 26.9% (1-90). ER, PR, HER2neu positivity was noted in 90/194 cases (46.4%), 74/194 cases (38.1%) and 110/194 cases (56.70%) respectively. Significant association was found between Ki67 and tumor grade, PR, HER2neu positivity and lymph node status, but no link was apparent with ER positivity and tumor size. There wasan inverse relation between Ki67 index and PR positivity, whereas a direct correlation was seen with HER2neu positivity. However, high Ki67 (>30%) was associated with decreased HER2neu positivity as compared to intermediate Ki67 (16-30%). The same trend was established with lymph node metastasis. Conclusion: Our study indicates that with high grade tumors, clinical utility of ki67 is greater in combination with other prognostic markers because we found that tumors with Ki67 higher than 30% have better prognostic profile compared to tumors with intermediate Ki67 level, as reflected by slightly lower frequency of lymph node metastasis and HER2neu expression. Therefore we suggest that Ki67 index should be categorized into high, intermediate and low groups when considering adjuvant chemotherapy and prognostic stratification.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.11
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• pp.5469-5475
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• 2012

Background and Objectives: Acute lymphoblastic leukemia (ALL) is a complex genetic disease involving many fusion oncogenes (FO) having prognostic significance. The frequency of various FO can vary in different ethnic groups, with important implications for prognosis, drug selection and treatment outcome. Method: We studied fusion oncogenes in 101 pediatric ALL patients using interphase FISH and RT-PCR, and their associations with clinical features and treatment outcome. Results: Five most common fusion genes i.e. BCR-ABL t (22; 9), TCF3-PBX1 (t 1; 19), ETV6-RUNX1 (t 12; 21), MLL-AF4 (t 4; 11) and SIL-TAL1 (del 1p32) were found in 89/101 (88.1%) patients. Frequency of BCR-ABL was 44.5% (45/101). BCR-ABL positive patients had a significantly lower survival ($43.7{\pm}4.24$ weeks) and higher white cell count as compared to others, except patients with MLL-AF4. The highest relapse-free survival was documented with ETV6-RUNX1 (14.2 months) followed closely by those cases in which no gene was detected (13.100). RFS with BCR-ABL, MLL-AF4, TCF3-PBX1 and SIL-TAL1 was less than 10 months (8.0, 3.6, 5.5 and 8.1 months, respectively). Conclusions: This is the first study from Pakistan correlating molecular markers with disease biology and treatment outcome in pediatric ALL. It revealed the highest reported frequency of BCR-ABL FO in pediatric ALL, associated with poor overall survival. Our data indicate an immediate need for incorporation of tyrosine kinase inhibitors in the treatment of BCR-ABL+ pediatric ALL in this population and the development of facilities for stem cell transplantation.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.17
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• pp.7967-7973
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• 2015

Background: The abrupt rise of colorectal cancer in developing countries is raising concern in healthcare settings. Studies on assessing relationships with modifiable and non-modifiable risk factors in the Pakistani population have been limited. The present investigation was designed to examine associations of dietary practices, addictive behavior and bowel habits in developing colorectal cancer (CRC) among patients in a low-resource setup. Materials and Methods: An age-gender matched case control study was conducted from October 2011 to July 2015 in Karachi, Pakistan. Cases were from the surgical oncology department of a public sector tertiary care hospital, while their two pair-matched controls were recruited from the general population. A structured questionnaire was used which included questions related to demographic characteristics, family history, dietary patterns, addictive behavior and bowel habits. Results: A family history of cancer was associated with a 2.2 fold higher chance of developing CRC. Weight loss reduced the likelihood 7.6 times. Refraining from a high fat diet and consuming more vegetables showed protective effects for CRC. The risk of CRC was more than twice among smokers and those who consumed Asian specific addictive products as compared to those who avoid using these addictions (ORsmoking: 2.12, 95% CI: 1.08 - 4.17, ORpan: 2.92, 95% CI: 1.6 - 5.33, ORgutka: 2.13, 95% CI: 1.14 - 3.97). Use of NSAID attenuated risk of CRC up to 86% (OR: 0.14, 95% CI: 0.07 - 0.31). Conclusions: Most of the findings showed concordance with the literature elucidating protective effects of consuming vegetables and low fat diet while documenting adverse associations with family history, weight loss, constipation and hematochezia. Moreover, this study highlighted Asian specific indigenous addictive products as important factors. Further studies are needed to validate the findings produced by this research.

• Journal of Life Science
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• v.31 no.5
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• pp.453-463
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• 2021

Hearing loss is a group of clinically and genetically heterogeneous disorders characterized by congenital- to adult-onset deafness with frequent additional symptoms such as myopathy, nephropathy, and optic disorders. It is commonly divided into two types: syndromic, with no other symptoms, and nonsyndromic, with other symptoms. Autosomal recessive hearing loss is relatively frequent in Pakistan, which may be due in part to frequent consanguineous marriages. This study was performed by whole exome sequencing to determine the genetic causes in two Pakistani consanguineous families with autosomal recessive hearing loss. We identified a pathogenic homozygous variant (p.Leu326Gln in MYO7A) in a family with prelingual-onset hearing loss and two variants of uncertain significance (p.Val3094Ile in GPR98 and p.Asp56Gly in PLA2G6) in a family with early-onset hearing loss concurrent with muscular atrophy. The missense mutations in MYO7A and PLA2G6 were located in the highly conserved sites, and in silico analyses predicted pathogenicity, while the GPR98 mutation was located in the less conserved site, and most in silico analysis programs predicted its nonpathogenic effect. Homozygosity mapping showed that both alleles of the homozygous mutations identified in each family originated from a single founder; spread from this single source might be due to consanguineous marriages. This study will help provide exact molecular diagnosis and treatment for autosomal recessive hearing loss patients in Pakistan.