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Article ; Online: Contribution of germline PALB2 variants to an unselected and prospectively registered pancreatic cancer patient cohort in Pakistan.

Muhammad, Noor / Sadaqat, Rida / Naeemi, Humaira / Masood, Iqra / Hassan, Usman / Ijaz, Bushra / Hanif, Faisal / Syed, Aamir A / Yusuf, Muhammed A / Rashid, Muhammad U

HPB : the official journal of the International Hepato Pancreato Biliary Association

2022 Volume 24, Issue 12, Page(s) 2134–2144

Abstract: Background: Partner and localizer of BRCA2 (PALB2) is a pancreatic cancer (PC) susceptibility gene reported in Caucasians. However, limited data are available among Asians. We investigated the contribution of PALB2 germline variants to Pakistani PC ... ...

Abstract	Background: Partner and localizer of BRCA2 (PALB2) is a pancreatic cancer (PC) susceptibility gene reported in Caucasians. However, limited data are available among Asians. We investigated the contribution of PALB2 germline variants to Pakistani PC patients. Methods: 150 unselected and prospectively enrolled PC patients were comprehensively screened for PALB2 variants, using denaturing high-performance liquid chromatography and DNA sequencing. Novel variants were investigated for their pathogenic effect using in-silico tools. Potentially functional variants were screened in 200 controls. Results: Twenty-two different PALB2 variants were identified. A missense variant (p.Arg37His) was identified in a 48-years-old male patient with a family history of breast cancer. Another missense variant (p.Trp898Arg) was identified in a 48-years-old male patient with a family history of esophageal cancer. A novel 3' downstream variant (c.∗480A>G) was detected in a 34-years-old female patient with family history of lung cancer. Another novel 3' downstream variant (c.∗417A>C) was identified in a 41-years-old male patient. All these variants were absent in 200 controls. p.Arg37His and p.Trp898Arg were predicted as likely pathogenic. c.∗417A>C and c.∗480A>G were classified as variants of uncertain significance. Conclusion: This is the first study that suggests a minimal contribution of PALB2 variants to PC risk in Pakistani population.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Middle Aged ; DNA Mutational Analysis ; Fanconi Anemia Complementation Group N Protein/genetics ; Genetic Predisposition to Disease ; Germ-Line Mutation ; Pancreatic Neoplasms/genetics ; Pancreatic Neoplasms
Chemical Substances	Fanconi Anemia Complementation Group N Protein ; PALB2 protein, human
Language	English
Publishing date	2022-09-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2131251-5
ISSN	1477-2574 ; 1365-182X
ISSN (online)	1477-2574
ISSN	1365-182X
DOI	10.1016/j.hpb.2022.09.003
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Article ; Online: Absence of the FANCM c.5101C>T mutation in BRCA1/2-negative triple-negative breast cancer patients from Pakistan.

Rashid, Muhammad U / Muhammad, Noor / Khan, Faiz A / Hamann, Ute

Breast cancer research and treatment

2015 Volume 152, Issue 1, Page(s) 229–230

MeSH term(s)	DNA Helicases/genetics ; Female ; Genes, BRCA1 ; Genes, BRCA2 ; Humans ; Mutation ; Pakistan ; Triple Negative Breast Neoplasms/diagnosis ; Triple Negative Breast Neoplasms/genetics
Chemical Substances	FANCM protein, human (EC 3.6.1.-) ; DNA Helicases (EC 3.6.4.-)
Language	English
Publishing date	2015-07
Publishing country	Netherlands
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-015-3457-5
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Article ; Online: Absence of the TRIP13 c.1060C>T Mutation in Wilms Tumor Patients From Pakistan.

Rashid, Muhammad U / Naeemi, Humaira / Qazi, Abid Q / Muhammad, Noor / Ahmad, Mansoor / Akhtar, Noreen / Rahman, Nazneen

Journal of pediatric hematology/oncology

2019 Volume 42, Issue 3, Page(s) e128–e131

Abstract: Background and aim: Wilms tumor (WT) is the most common childhood malignant renal tumor. Germline mutations in several WT predisposition genes have been identified. However, the fundamental cause of most WT patients remains unexplained. Recently, a ... ...

Abstract	Background and aim: Wilms tumor (WT) is the most common childhood malignant renal tumor. Germline mutations in several WT predisposition genes have been identified. However, the fundamental cause of most WT patients remains unexplained. Recently, a founder mutation, c.1060C>T (p. Arg254X) in a mitotic spindle checkpoint gene, TRIP13, was reported in 5 unrelated children with WT from the United Kingdom, of Pakistani descent from Azad Kashmir region. This observation suggests other children with WT in Pakistan may also harbor this mutation. We conducted the first study to assess the contribution of TRIP13 c.1060C>T mutation to WT in Pakistan. Materials and methods: Constitutional genomic DNA from 68 Pakistani individuals including unrelated WT cases (n=26) and one (n=10) or both (n=32) of their parent(s) were screened for the TRIP13 c.1060C>T mutation using DNA sequence analysis. We also included positive controls in the analyses. Results: The median age of WT diagnosis was 3.0 years (range, 0.75 to 10). The TRIP13 c.1060C>T mutation was not found in any WT patient (n=26) or their parents (n=42). Twenty-four patients (92.4%) presented with unilateral tumor and 2 patients (7.7%) were diagnosed with synchronous bilateral WT. Thirteen patients (50%) reported parental consanguinity. Thirteen patients (50.0%) belonged to the Punjabi ethnicity and 1 patient (3.8%) had a Kashmiri background. Four patients (16.7%) reported a family history of WT or other malignancies. The predominant histologic subtype was stromal (46.2%). The majority of patients presented with >5 cm of tumor size (81%). None of the patients had a personal or family history of congenital anomalies, or associated genetic syndromes. Conclusions: Our findings suggest that TRIP13 c.1060C>T mutation may be infrequent in Pakistani WT cases. Further evaluation of this mutation in a large number of WT patients of Kashmiri heritage and various ethnic backgrounds from Pakistan is warranted.
MeSH term(s)	ATPases Associated with Diverse Cellular Activities/genetics ; Cell Cycle Proteins/genetics ; Child ; Child, Preschool ; Female ; Genes, Wilms Tumor ; Genetic Predisposition to Disease/genetics ; Humans ; Infant ; Kidney Neoplasms/genetics ; Male ; Mutation ; Pakistan ; Wilms Tumor/genetics
Chemical Substances	Cell Cycle Proteins ; ATPases Associated with Diverse Cellular Activities (EC 3.6.4.-) ; TRIP13 protein, human (EC 3.6.4.-)
Language	English
Publishing date	2019-09-30
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1231152-2
ISSN	1536-3678 ; 1077-4114 ; 0192-8562
ISSN (online)	1536-3678
ISSN	1077-4114 ; 0192-8562
DOI	10.1097/MPH.0000000000001602
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Article ; Online: Contribution of BRCA1 large genomic rearrangements to early-onset and familial breast/ovarian cancer in Pakistan.

Rashid, Muhammad U / Muhammad, Noor / Amin, Asim / Loya, Asif / Hamann, Ute

Breast cancer research and treatment

2017 Volume 161, Issue 2, Page(s) 191–201

Abstract: Background: Germline mutations in BRCA1 and BRCA2 (BRCA1/2) account for the majority of hereditary breast and/or ovarian cancers. Pakistan has one of the highest rates of breast cancer incidence in Asia, where BRCA1/2 small-range mutations account for ... ...

Abstract	Background: Germline mutations in BRCA1 and BRCA2 (BRCA1/2) account for the majority of hereditary breast and/or ovarian cancers. Pakistan has one of the highest rates of breast cancer incidence in Asia, where BRCA1/2 small-range mutations account for 17% of early-onset and familial breast/ovarian cancer patients. We report the first study from Pakistan evaluating the prevalence of BRCA1/2 large genomic rearrangements (LGRs) in breast and/or ovarian cancer patients who do not harbor small-range BRCA1/2 mutations. Materials and methods: Both BRCA1/2 genes were comprehensively screened for LGRs using multiplex ligation-dependent probe amplification in 120 BRCA1/2 small-range mutations negative early-onset or familial breast/ovarian cancer patients from Pakistan (Group 1). The breakpoints were characterized by long-range PCR- and DNA-sequencing analyses. An additional cohort of 445 BRCA1/2 negative high-risk patients (Group 2) was analyzed for the presence of LGRs identified in Group 1. Results: Three different BRCA1 LGRs were identified in Group 1 (4/120; 3.3%), two of these were novel. Exon 1-2 deletion was observed in two unrelated patients: an early-onset breast cancer patient and another bilateral breast cancer patient from a hereditary breast cancer (HBC) family. Novel exon 20-21 deletion was detected in a 29-year-old breast cancer patient from a HBC family. Another novel exon 21-24 deletion was identified in a breast-ovarian cancer patient from a hereditary breast and ovarian cancer family. The breakpoints of all deletions were characterized. Screening of the 445 patients in Group 2 for the three LGRs revealed ten additional patients harboring exon 1-2 deletion or exon 21-24 deletion (10/445; 2.2%). No BRCA2 LGRs were identified. Conclusions: LGRs in BRCA1 are found with a considerable frequency in Pakistani breast/ovarian cancer cases. Our findings suggest that BRCA1 exons 1-2 deletion and exons 21-24 deletion should be included in the recurrent BRCA1/2 mutations panel for genetic testing of high-risk Pakistani breast/ovarian cancer patients.
Language	English
Publishing date	2017-01
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-016-4044-0
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Article ; Online: Deleterious RAD51C germline mutations rarely predispose to breast and ovarian cancer in Pakistan.

Rashid, Muhammad U / Muhammad, Noor / Faisal, Saima / Amin, Asim / Hamann, Ute

Breast cancer research and treatment

2014 Volume 145, Issue 3, Page(s) 775–784

Abstract: RAD51C plays a key role in homologous recombination-mediated DNA repair and maintenance of genomic stability. Biallelic RAD51C mutations cause Fanconi anemia, and monoallelic mutations predispose women to breast and ovarian cancer. Genetic variability of ...

Abstract	RAD51C plays a key role in homologous recombination-mediated DNA repair and maintenance of genomic stability. Biallelic RAD51C mutations cause Fanconi anemia, and monoallelic mutations predispose women to breast and ovarian cancer. Genetic variability of RAD51C and its impact in Asian populations have been poorly studied. Here, we report the results of comprehensive mutational screening of the RAD51C gene in 348 BRCA1/2-negative breast and/or ovarian cancer patients from Pakistan. Mutation analysis of the complete RAD51C-coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. Three novel protein-truncating mutations, c.204T>A, c.225T>G, and c.701C>G, were identified. c.204T>A was found in one out of 22 (4.5 %) early-onset (≤45 years of age) ovarian cancer patients and c.225T>G in one out of 119 (0.8 %) patients from breast cancer only families. c.701C>G was found in a 60-year-old control with no family history of breast/ovarian cancer. Furthermore, three novel in silico-predicted potentially functional mutations, a missense mutation, c.873T>G, a variant in 5'UTR, c.1-34T>G, and a recurrent intronic variant, c.965+21A>G, were identified. The missense mutation was observed in a patient with bilateral breast cancer from a breast and ovarian cancer family (HBOC), the 5'UTR variant was noted in an early-onset breast cancer patient, and the intronic variant in one early-onset breast cancer patient and one ovarian cancer patient from a HBOC family. Five of the six mutations described were not detected in 400 healthy controls. These findings suggest that RAD51C plays a marginal role in breast and ovarian cancer predisposition in Pakistan. Reliable estimation of the clinical implications of carrying a deleterious RAD51C mutation will require identification of additional mutation-positive patients/families.
MeSH term(s)	Adult ; Aged ; Base Sequence ; Breast Neoplasms/genetics ; DNA Mutational Analysis ; DNA-Binding Proteins/genetics ; Female ; Gene Frequency ; Genetic Predisposition to Disease ; Humans ; Middle Aged ; Mutation ; Ovarian Neoplasms/genetics ; Pakistan ; Sequence Analysis, DNA ; Young Adult
Chemical Substances	DNA-Binding Proteins ; RAD51C protein, human
Language	English
Publishing date	2014-06
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-014-2972-0
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Article: A novel deleterious c.2656G>T MSH2 germline mutation in a Pakistani family with a phenotypic overlap of hereditary breast and ovarian cancer and Lynch syndrome.

Rashid, Muhammad U / Naeemi, Humaira / Muhammad, Noor / Loya, Asif / Yusuf, Muhammed A / Lubiński, Jan / Jakubowska, Anna / Hamann, Ute

Hereditary cancer in clinical practice

2016 Volume 14, Page(s) 14

Abstract: Background: Hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome (LS) account for a significant proportion of inherited gynecologic malignancies, mainly caused by pathogenic germline mutations in the BRCA1 and BRCA2 genes or in ... ...

Abstract	Background: Hereditary breast and ovarian cancer syndrome (HBOC) and Lynch syndrome (LS) account for a significant proportion of inherited gynecologic malignancies, mainly caused by pathogenic germline mutations in the BRCA1 and BRCA2 genes or in mismatch repair (MMR) genes, such as MLH1 and MSH2. Women harboring deleterious mutations in these genes have increased life-time risks of developing a number of malignancies including ovarian cancer. Since there is a phenotypic overlap of HBOC and LS, timely identification of individuals at-risk of a particular syndrome is crucial in order to optimize cancer risk management. Case presentation: We report a novel pathogenic MSH2 mutation, c.2656G > T, which was identified in a 67-year-old female patient with breast cancer, who had previously tested negative for a deleterious mutation in the breast cancer susceptibility genes BRCA1, BRCA2, CHEK2 or RAD51C. The patient reported a personal history of endometrial cancer diagnosed at age 48, and a strong family history of breast and ovarian cancer, as well as several other malignancies within the spectrum of LS. The novel mutation was also found in the index patient's daughter and a niece, who were diagnosed with endometrial and ovarian cancer, respectively. Breast and endometrial tumors from c.2656G > T mutation carriers showed loss of MSH2 and MSH6 protein expression. The mutation was absent in the control population. Conclusions: Our finding suggests that testing for MMR genes may be of benefit to BRCA1/2 negative families with overlapping HBOC and LS phenotype in Pakistan. It is clinically significant to identify individuals harboring mutations in genes linked with a particular syndrome so that they can benefit from targeted life-saving cancer surveillance and preventive strategies.
Language	English
Publishing date	2016-07-12
Publishing country	Poland
Document type	Case Reports
ZDB-ID	2252512-9
ISSN	1897-4287 ; 1731-2302
ISSN (online)	1897-4287
ISSN	1731-2302
DOI	10.1186/s13053-016-0056-3
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Article ; Online: Constitutional CHEK2 mutations are infrequent in early-onset and familial breast/ovarian cancer patients from Pakistan.

Rashid, Muhammad U / Muhammad, Noor / Faisal, Saima / Amin, Asim / Hamann, Ute

BMC cancer

2013 Volume 13, Page(s) 312

Abstract: Background: Less than 20% of Pakistani women with early-onset or familial breast/ovarian cancer harbor germ line mutations in the high-penetrance genes BRCA1, BRCA2 and TP53. Thus, mutations in other genes confer genetic susceptibility to breast cancer, ...

Abstract	Background: Less than 20% of Pakistani women with early-onset or familial breast/ovarian cancer harbor germ line mutations in the high-penetrance genes BRCA1, BRCA2 and TP53. Thus, mutations in other genes confer genetic susceptibility to breast cancer, of which CHEK2 is a plausible candidate. CHEK2 encodes a checkpoint kinase, involved in response to DNA damage. Methods: In the present study we assessed the prevalence of CHEK2 germ line mutations in 145 BRCA1/2-negative early-onset and familial breast/ovarian cancer patients from Pakistan (Group 1). Mutation analysis of the complete CHEK2 coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. Results: Two potentially deleterious missense mutations, c.275C>G (p.P92R) and c.1216C>T, (p.R406C), were identified (1.4%). The c.275C>G mutation is novel and has not been described in other populations. It was detected in a 30-year-old breast cancer patient with a family history of breast and multiple other cancers. The c.1216C>T mutation was found in a 34-year-old ovarian cancer patient from a family with two breast cancer cases. Both mutations were not detected in 229 recently recruited BRCA1/2-negative high risk patients (Group 2). Conclusion: Our findings suggest that CHEK2 mutations may not contribute significantly to breast/ovarian cancer risk in Pakistani women.
MeSH term(s)	Adult ; Aged ; Breast Neoplasms/genetics ; Breast Neoplasms, Male/genetics ; Checkpoint Kinase 2/genetics ; DNA Mutational Analysis ; Female ; Germ-Line Mutation ; Humans ; Male ; Middle Aged ; Mutation, Missense ; Ovarian Neoplasms/genetics ; Pakistan ; Young Adult
Chemical Substances	Checkpoint Kinase 2 (EC 2.7.1.11)
Language	English
Publishing date	2013-06-27
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1471-2407
ISSN (online)	1471-2407
DOI	10.1186/1471-2407-13-312
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Article ; Online: Prevalence of TP53 germ line mutations in young Pakistani breast cancer patients.

Rashid, Muhammad U / Gull, Sidra / Asghar, Kashif / Muhammad, Noor / Amin, Asim / Hamann, Ute

Familial cancer

2012 Volume 11, Issue 2, Page(s) 307–311

Abstract: Women from Pakistan and India are more often diagnosed with early-onset breast cancer than Caucasian women. Given that only 12% of Pakistani women diagnosed with breast cancer at or before 30 years of age have previously been shown to harbor germ line ... ...

Abstract	Women from Pakistan and India are more often diagnosed with early-onset breast cancer than Caucasian women. Given that only 12% of Pakistani women diagnosed with breast cancer at or before 30 years of age have previously been shown to harbor germ line mutations in the breast cancer susceptibility genes BRCA1 and BRCA2, the genetic causes of the majority of early-onset cases are unexplained. Since germ line mutations in the tumor suppressor gene TP53 predispose women to early-onset breast cancer, we assessed the prevalence of TP53 mutations in 105 early-onset breast cancer patients from Pakistan, who had previously been found to be negative for BRCA1 and BRCA2 germ line mutations. The patient group included 67 women diagnosed with early-onset breast cancer at or before age 30 with no family history of breast or ovarian cancer (EO30NFH group) and 38 women diagnosed with breast cancer at or before age 40 with one or more first- or second-degree relatives with breast or ovarian cancer (EO40FH group). Mutation analysis of the complete TP53 coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. One deleterious mutation, c.499-500delCA in exon 5, was identified in the 105 breast cancer patients (1%). This mutation is novel in the germ line and has not been described in other populations. It was detected in a 28-year-old patient with no family history of breast or ovarian cancer. This mutation is rare as it was not detected in additional 157 recently recruited non-BRCA1 and non-BRCA2-associated early-onset breast cancer patients. Our findings show that TP53 mutations may account for a minimal portion of early-onset breast cancer in Pakistan.
MeSH term(s)	Adult ; Age of Onset ; Breast Neoplasms/epidemiology ; Breast Neoplasms/genetics ; Female ; Germ-Line Mutation ; Humans ; Pakistan/epidemiology ; Tumor Suppressor Protein p53/genetics ; Young Adult
Chemical Substances	Tumor Suppressor Protein p53
Language	English
Publishing date	2012-02-05
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1502496-9
ISSN	1573-7292 ; 1389-9600
ISSN (online)	1573-7292
ISSN	1389-9600
DOI	10.1007/s10689-012-9509-7
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Article ; Online: A deleterious BRCA1 mutation in a young Pakistani woman with metaplastic breast carcinoma.

Rashid, Muhammad U / Shah, Mazher A / Azhar, Rafay / Syed, Aamir A / Amin, Asim / Hamann, Ute

Pathology, research and practice

2011 Volume 207, Issue 9, Page(s) 583–586

Abstract: Metaplastic breast carcinoma (MBC) is a relatively rare subtype of breast cancer that encompasses a pathologically heterogeneous group of tumors. Pathogenic germ line mutations in the major breast cancer susceptibility genes BRCA1 and BRCA2 genes have ... ...

Abstract	Metaplastic breast carcinoma (MBC) is a relatively rare subtype of breast cancer that encompasses a pathologically heterogeneous group of tumors. Pathogenic germ line mutations in the major breast cancer susceptibility genes BRCA1 and BRCA2 genes have been rarely found or described in MBC. We report the identification of the BRCA1 185delAG mutation in a 22-year-old Pakistani woman with triple-negative MBC that showed biphasic morphological features, including sarcomatous and malignant epithelial components. A comprehensive description of the clinical, histopathological, morphological, and immunohistochemical features of the tumor and the patient's treatment course is presented.
MeSH term(s)	BRCA1 Protein/genetics ; BRCA1 Protein/metabolism ; Biomarkers, Tumor/metabolism ; Breast Neoplasms/genetics ; Breast Neoplasms/metabolism ; Breast Neoplasms/pathology ; Breast Neoplasms/therapy ; Carcinoma, Ductal, Breast/genetics ; Carcinoma, Ductal, Breast/metabolism ; Carcinoma, Ductal, Breast/pathology ; Carcinoma, Ductal, Breast/therapy ; Combined Modality Therapy ; Disease-Free Survival ; Female ; Germ-Line Mutation ; Humans ; Mastectomy, Modified Radical ; Metaplasia ; Sarcoma/genetics ; Sarcoma/metabolism ; Sarcoma/pathology ; Sarcoma/therapy ; Treatment Outcome
Chemical Substances	BRCA1 Protein ; BRCA1 protein, human ; Biomarkers, Tumor
Language	English
Publishing date	2011-09-15
Publishing country	Germany
Document type	Case Reports ; Journal Article
ZDB-ID	391889-0
ISSN	1618-0631 ; 0344-0338
ISSN (online)	1618-0631
ISSN	0344-0338
DOI	10.1016/j.prp.2011.05.011
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Article ; Online: Absence of the BRCA1 del (exons 9-12) mutation in breast/ovarian cancer families outside of Mexican Hispanics.

Torres, Diana / Rashid, Muhammad U / Seidel-Renkert, Antje / Weitzel, Jeffrey N / Briceno, Ignacio / Hamann, Ute

Breast cancer research and treatment

2009 Volume 117, Issue 3, Page(s) 679–681

MeSH term(s)	Adolescent ; Adult ; Aged ; Breast Neoplasms/ethnology ; Breast Neoplasms/genetics ; Breast Neoplasms, Male/ethnology ; Breast Neoplasms, Male/genetics ; Colombia/ethnology ; Female ; Founder Effect ; Genes, BRCA1 ; Germany/ethnology ; Hispanic Americans/ethnology ; Hispanic Americans/genetics ; Humans ; Male ; Mexico/ethnology ; Middle Aged ; Ovarian Neoplasms/ethnology ; Ovarian Neoplasms/genetics ; Pakistan/ethnology ; Sequence Deletion ; Young Adult
Language	English
Publishing date	2009-10
Publishing country	Netherlands
Document type	Letter ; Research Support, Non-U.S. Gov't
ZDB-ID	604563-7
ISSN	1573-7217 ; 0167-6806
ISSN (online)	1573-7217
ISSN	0167-6806
DOI	10.1007/s10549-009-0383-4
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