BackgroundThe contribution of genetic factors to the development of breast cancer in the admixed and consanguineous population of the western region of Saudi Arabia is thought to be significant as the disease is early onset. The current protocols of continuous clinical follow-up of relatives of such patients are costly and cause a burden on the usually over-stretched medical resources. Discovering the significant contribution of BRCA1/2 mutations to breast cancer susceptibility allowed for the design of genetic tests that allows the medical practitioner to focus the care for those who need it most. However, BRCA1/2 mutations do not account for all breast cancer susceptibility genes and there are other genetic factors, known and unknown that may play a role in the development of such disease. The advent of whole-exome sequencing is offering a unique opportunity to identify the breast cancer susceptibility genes in each family of sufferers. The polymorphisms/mutations identified will then allow for personalizing the genetic screening tests accordingly. To this end, we have performed whole-exome sequencing of seven breast cancer patients with positive family history of the disease using the Agilent SureSelect™ Whole-Exome Enrichment kit and sequencing on the SOLiD™ platform.ResultsWe have identified several coding single nucleotide variations that were either novel or rare affecting genes controlling DNA repair in the BRCA1/2 pathway.ConclusionThe disruption of DNA repair pathways is very likely to contribute to breast cancer susceptibility in the Saudi population.

The Third International Genomic Medicine Conference (3rd IGMC) was organised by the Centre of Excellence in Genomic Medicine Research (CEGMR) at the King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia (KSA). This conference is a continuation of a series of meetings, which began with the first International Genomic Medicine Conference (1st IGMC, 2011) followed by the second International Genomic Medicine Conference (2nd IGMC, 2013). The 3rd IGMC meeting presented as a timely opportunity to bring scientists from across the world to gather, discuss, and exchange recent advances in the field of genomics and genetics in general as well as practical information on using these new technologies in different basic and clinical applications. The meeting undoubtedly inspired young male and female Saudi researchers, who attended the conference in large numbers, as evidenced by the oversubscribed oral and poster presentations. The conference also witnessed the launch of the first content for npj Genomic Medicine, a high quality new journal was established in partnership by CEGMR with Springer Nature and published as part of the Nature Partner Journal series. Here, we present a brief summary report of the 2-day meeting including highlights from the oral presentations, poster presentations, workshops, poster prize-winners and comments from the distinguished scientists.

contentsO1 Regulation of genes by telomere length over long distancesJerry W. ShayO2 The microtubule destabilizer KIF2A regulates the postnatal establishment of neuronal circuits in addition to prenatal cell survival, cell migration, and axon elongation, and its loss leading to malformation of cortical development and severe epilepsyNoriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka HirokawaO3 Integration of metagenomics and metabolomics in gut microbiome researchMaryam Goudarzi, Albert J. Fornace Jr.O4 A unique integrated system to discern pathogenesis of central nervous system tumorsSaleh Baeesa, Deema Hussain, Mohammed Bangash, Fahad Alghamdi, Hans-Juergen Schulten, Angel Carracedo, Ishaq Khan, Hanadi Qashqari, Nawal Madkhali, Mohamad Saka, Kulvinder S. Saini, Awatif Jamal, Jaudah Al-Maghrabi, Adel Abuzenadah, Adeel Chaudhary, Mohammed Al Qahtani, Ghazi DamanhouriO5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesisHeba AlkhatabiO6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic serviceAnne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas BeauchampO7 Targeted sequencing panels and their utilization in personalized medicineAdel M. AbuzenadahO8 International biobanking in the era of precision medicineJim VaughtO9 Biobank and biodata for clinical and forensic applicationsBruce Budowle, Mourad Assidi, Abdelbaset BuhmeidaO10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumorsJaudah Al-MaghrabiO11 The CEGMR biobanking unit: achievements, challenges and future plansAbdelbaset Buhmeida, Mourad Assidi, Leena MerdadO12 Phylomedicine of tumorsSudhir Kumar, Sayaka Miura, Karen GomezO13 Clinical implementation of pharmacogenomics for colorectal cancer treatmentAngel Carracedo, Mahmood RasoolO14 From association to causality: translation of GWAS findings for genomic medicineAhmed RebaiO15 E-GRASP: an interactive database and web application for efficient analysis of disease-associated genetic informationSajjad Karim, Hend F Nour Eldin, Heba Abusamra, Elham M Alhathli, Nada Salem, Mohammed H Al-Qahtani, Sudhir KumarO16 The supercomputer facility “AZIZ” at KAU: utility and future prospectsHossam FaheemO17 New research into the causes of male infertilityAshok AgarwaO18 The Klinefelter syndrome: recent progress in pathophysiology and managementEberhard Nieschlag, Joachim Wistuba, Oliver S. Damm, Mohd A. Beg, Taha A. Abdel-Meguid, Hisham A. Mosli, Osama S. Bajouh, Adel M. Abuzenadah, Mohammed H. Al-QahtaniO19 A new look to reproductive medicine in the era of genomicsSerdar CoskunP1 Wnt signalling receptors expression in Saudi breast cancer patientsMuhammad Abu-Elmagd, Abdelbaset Buhmeida, Ashraf Dallol, Jaudah Al-Maghrabi, Sahar Hakamy, Wejdan Al-Qahtani, Asia Al-Harbi, Shireen Hussain, Mourad Assidi, Mohammed Al-Qahtani, Adel AbuzenadahP2 Analysis of oxidative stress interactome during spermatogenesis: a systems biology approach to reproductionBurak Ozkosem, Rick DuBoisP3 Interleukin-18 gene variants are strongly associated with idiopathic recurrent pregnancy loss.Safia S Messaoudi, Maryam T Dandana, Touhami Mahjoub, Wassim Y AlmawiP4 Effect of environmental factors on gene-gene and gene-environment reactions: model and theoretical study applied to environmental interventions using genotypeS. Abdalla, M. Nabil Al-AamaP5 Genomics and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumorAsmaa Elzawahry, Tsuyoshi Takahashi, Sachiyo Mimaki, Eisaku Furukawa, Rie Nakatsuka, Isao Kurosaka, Takahiko Nishigaki, Hiromi Nakamura, Satoshi Serada, Tetsuji Naka, Seiichi Hirota, Tatsuhiro Shibata, Katsuya Tsuchihara, Toshirou Nishida, Mamoru KatoP6 In-Silico analysis of putative HCV epitopes against Pakistani human leukocyte antigen background: an approach towards development of future vaccines for Pakistani populationSajid Mehmood, Naeem Mahmood Ashraf, Awais Asif, Muhammad Bilal, Malik Siddique Mehmood, Aadil HussainP7 Inhibition of AChE and BuChE with the natural compounds of Bacopa monerri for the treatment of Alzheimer’s disease: a bioinformatics approachQazi Mohammad Sajid Jamal, Mughees Uddin Siddiqui, Mohammad A. Alzohairy, Mohammad A. Al KaraawiP8 Her2 expression in urothelial cell carcinoma of the bladder in Saudi ArabiaTaoufik Nedjadi, Jaudah Al-Maghrabi, Mourad Assidi, Heba Al-Khattabi, Adel Al-Ammari, Ahmed Al-Sayyad, Abdelbaset Buhmeida, Mohammed Al-QahtaniP9 Association of angiotensinogen single nucleotide polymorphisms with Preeclampsia in patients from North AfricaHédia Zitouni, Nozha Raguema, Marwa Ben Ali, Wided Malah, Raja Lfalah, Wassim Almawi, Touhami MahjoubP10 Systems biology analysis reveals relations between normal skin, benign nevi and malignant melanomaMohammed Elanbari, Andrey PtitsynP11 The apoptotic effect of thymoquinone in Jurkat cellsSana Mahjoub, Rabeb El Ghali, Bechir Achour, Nidhal Ben Amor, Mourad Assidi, Brahim N'siri, Hamid MorjaniP12 Sonic hedgehog contributes in bladder cancer invasion in Saudi ArabiaTaoufik Nedjadi, Adel Al-Ammari, Ahmed Al-Sayyad, Nada Salem, Esam Azhar, Jaudah Al-MaghrabiP13 Association of Interleukin 18 gene promoter polymorphisms - 607A/C and -137 G/C with colorectal cancer onset in a sample of Tunisian populationVera Chayeb, Maryam Dendena, Hedia Zitouni, Khedija Zouari-Limayem, Touhami MahjoubP14 Pathological expression of interleukin-6, -11, leukemia inhibitory factor and their receptors in tubal gestation with and without tubal cytomegalovirus infectionBassem Refaat, Ahmed M Ashshi, Sarah A BatwaP15 Phenotypic and genetic profiling of avian pathogenic and human diarrhegenic Escherichia coli in EgyptHazem Ramadan, Amal Awad, Ahmed AteyaP16 Cancer-targeting dual gene virotherapy as a promising therapeutic strategy for treatment of hepatocellular carcinomaAdel Galal Ahmed El-Shemi, Ahmad Ashshi, Mohammed Basalamah, Youjin Na, Chae-Ok YUNP17 Cancer dual gene therapy with oncolytic adenoviruses expressing TRAIL and IL-12 transgenes markedly eradicated human hepatocellular carcinoma both in vitro and in vivoAdel Galal Ahmed El-Shemi, Ahmad Ashshi, Mohammed Basalamah, Youjin Na, Chae-Ok YunP18 Therapy with paricalcitol attenuates tumor growth and augments tumoricidal and anti-oncogenic effects of 5-fluorouracil on animal model of colon cancerAdel Galal El-Shemi, Bassem Refaat, Osama Kensara, Amr AbdelfattahP19 The effects of Rubus idaeus extract on normal human lymphocytes and cancer cell lineBatol Imran Dheeb, Mohammed M. F. Al-Halbosiy, Rghad Kadhim Al lihabi, Basim Mohammed KhashmanP20 Etanercept, a TNF-alpha inhibitor, alleviates mechanical hypersensitivity and spontaneous pain in a rat model of chemotherapy-induced neuropathic painDjouhri, Laiche, Chaudhary Adeel, Nedjadi, TaoufikP21 Sleeping beauty mutagenesis system identified genes and neuronal transcription factor network involved in pediatric solid tumour (medulloblastoma)Hani Al-Afghani, Maria Łastowska, Haya H Al-Balool, Harsh Sheth, Emma Mercer, Jonathan M Coxhead, Chris PF Redfern, Heiko Peters, Alastair D Burt, Mauro Santibanez-Koref, Chris M Bacon, Louis Chesler, Alistair G Rust, David J Adams, Daniel Williamson, Steven C Clifford, Michael S JacksonP22 Involvement of interleukin-1 in vitiligo pathogenesisMala Singh, Mohmmad Shoab Mansuri, Shahnawaz D. Jadeja, Hima Patel, Yogesh S. Marfatia, Rasheedunnisa BegumP23 Cytogenetics abnormalities in 12,884 referred population for chromosomal analysis and the role of FISH in refining the diagnosis (cytogenetic experience 2004-2013)Amal M Mohamed, Alaa K Kamel, Nivin A Helmy, Sayda A Hammad, Hesham F Kayed, Marwa I Shehab, Assad El Gerzawy, Maha M. Ead, Ola M Ead, Mona Mekkawy, Innas Mazen, Mona El-RubyP24 Analysis of binding properties of angiotensin-converting enzyme 2 through in silico methodS. M. A. Shahid, Qazi Mohammad Sajid Jamal, J. M. Arif, Mohtashim LohaniP25 Relationship of genetics markers cis and trans to the β-S globin gene with fetal hemoglobin expression in Tunisian sickle cell patientsMoumni Imen, Chaouch Leila, Ouragini Houyem, Douzi Kais, Chaouachi Dorra Mellouli Fethi, Bejaoui Mohamed, Abbes SalemP26 Analysis of estrogen receptor alpha gene polymorphisms in breast cancer: link to genetic predisposition in Sudanese womenAreeg Faggad, Amanuel T Gebreslasie, Hani Y Zaki, Badreldin E AbdallaP27 KCNQI gene polymorphism and its association with CVD and T2DM in the Saudi populationMaha S AlShammari, Rhaya Al-Ali, Nader Al-Balawi , Mansour Al-Enazi, Ali Al-Muraikhi, Fadi Busaleh, Ali Al-Sahwan, Francis Borgio, Abdulazeez Sayyed, Amein Al-Ali, Sadananda AcharyaP28 Clinical, neuroimaging and cytogenetic study of a patient with microcephaly capillary malformation syndromeMaha S. Zaki, Hala T. El-Bassyouni, Marwa I. ShehabP29 Altered expression of CD200R1 on dendritic cells of patients with inflammatory bowel diseases: in silico investigations and clinical evaluationsMohammed F. Elshal, Kaleemuddin M., Alia M. Aldahlawi, Omar Saadah,J. Philip McCoyP30 Development of real time PCR diagnostic protocol specific for the Saudi Arabian H1N1 viral strainsAdel E El-Tarras, Nabil S Awad, Abdulla A Alharthi, Mohamed M M IbrahimP31 Identification of novel genetic variations affecting Osteoarthritis patientsHaneen S Alsehli, Ashraf Dallol, Abdullah M Gari, Mohammed M Abbas, Roaa A Kadam, Mazen M. Gari, Mohmmed H Alkaff, Adel M Abuzenadah, Mamdooh A GariP32 An integrated database of GWAS SNVs and their evolutionary propertiesHeba Abusamra, Sajjad Karim, Hend F Nour eldin, Elham M Alhathli, Nada Salem, Sudhir Kumar, Mohammed H Al-QahtaniP33 Familial hypercholesterolemia in Saudi Arabia: prime time for a national registry and genetic analysisFatima A. Moradi, Omran M. Rashidi, Zuhier A. AwanP34 Comparative genomics and network-based analyses of early hepatocellular carcinomaIbrahim Hamza Kaya, Olfat Al-Harazi, Dilek ColakP35 A TALEN-based oncolytic viral vector approach to knock out ABCB1 gene mediated chemoresistance in cancer stem cellsNabila A Alkousi, Takis AthanasopoulosP36 Cartilage differentiation and gene expression of synovial fluid mesenchymal stem cells derived from osteoarthritis patientsAfnan O Bahmaid, Etimad A Alhwait, Mamdooh A Gari, Haneen S Alsehli, Mohammed M Abbas, Mohammed H Alkaf, Roaa Kadam, Ashraf Dallol, Gauthaman KalamegamP37 E-GRASP: Adding an evolutionary component to the genome-wide repository of associations (GRASP) resourceHend F Nour Eldin, Sajjad Karim, Heba Abusamra, Elham Alhathli, Nada Salem, Mohammed H Al-Qahtani, Sudhir KumarP38 Screening of AGL gene mutation in Saudi family with glycogen storage disease Type IIISalma N Alsayed, Fawziah H Aljohani, Samaher M Habeeb, Rawan A Almashali, Sulman Basit, Samia M AhmedP39 High throughput proteomic data suggest modulation of cAMP dependent protein kinase A and mitochondrial function in infertile patients with varicoceleRakesh Sharma, Ashok Agarwal, Damayanthi Durairajanayagam, Luna Samanta, Muhammad Abu-Elmagd, Adel M. Abuzenadah, Edmund S. Sabanegh, Mourad Assidi, Mohammed Al-QahtaniP40 Significant protein profile alterations in men with primary and secondary infertilityAshok Agarwal, Rakesh Sharma, Luna Samanta, Damayanthi Durairajanayagam, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-Qahtani, Adel M. Abuzenadah, Edmund S. SabaneghP41 Spermatozoa maturation in infertile patients involves compromised expression of heat shock proteinsLuna Samanta, Ashok Agarwal, Rakesh Sharma, Zhihong Cui, Mourad Assidi, Adel M. Abuzenadah, Muhammad Abu-Elmagd, Mohammed Al-QahtaniP42 Array comparative genomic hybridization approach to search genomic answers for spontaneous recurrent abortion in Saudi ArabiaAlaa A Alboogmi, Nuha A Alansari, Maha M Al-Quaiti, Fai T Ashgan, Afnan Bandah, Hasan S Jamal, Abdullraheem Rozi, Zeenat Mirza, Adel M Abuzenadah, Sajjad Karim, Mohammed H Al-QahtaniP43 Global gene expression profiling of Saudi kidney cancer patientsSajjad Karim, Hans-Juergen Schulten, Ahmad J Al Sayyad, Hasan MA Farsi, Jaudah A Al-Maghrabi, Zeenat Mirza, Reem Alotibi, Alaa Al-Ahmadi, Nuha A Alansari, Alaa A Albogmi, Maha M Al-Quaiti, Fai T Ashgan, Afnan Bandah, Mohammed H Al-QahtaniP44 Downregulated StAR gene and male reproductive dysfunction caused by nifedipine and ethosuximideRasha A Ebiya, Samia M Darwish, Metwally M. MontaserP45 Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genesHeba Abusamra, Vladimir B. BajicP46 Prognostic significance of Osteopontin expression profile in colorectal carcinomaJaudah Al-Maghrabi, Wafaey Gomaa, Mehenaz Hanbazazh, Mahmoud Al-Ahwal, Asia Al-Harbi, Wejdan Al-Qahtani, Saher Hakamy, Ghali Baba, Abdelbaset Buhmeida, Mohammed Al-QahtaniP47 High Glypican-3 expression pattern predicts longer disease-specific survival in colorectal carcinomaJaudah Al-Maghrabi, Abdullah Al-Harbi, Mahmoud Al-Ahwal, Asia Al-Harbi, Wejdan Al-Qahtani, Sahar Hakamy, Ghalia Baba, Abdelbaset Buhmeida, Mohammed Al-QahtaniP48 An evolutionary re-assessment of GWAS single nucleotide variants implicated in the Cholesterol traitsElham M Alhathli, Sajjad Karim, Nada Salem, Hend Nour Eldin, Heba Abusamra, Sudhir Kumar, Mohammed H Al-QahtaniP49 Derivation and characterization of human Wharton’s jelly stem cells (hWJSCs) in vitro for future therapeutic applicationsAisha A Alyamani, Gauthaman Kalamegam, Etimad A Alhwait, Mamdooh A Gari, Mohammed M Abbas, Mohammed H Alkaf, Haneen S Alsehli, Roaa A Kadam, Mohammed Al-QahtaniP50 Attitudes of healthcare students toward biomedical research in the post-genomic eraRawan Gadi, Abdelbaset Buhmeida, Mourad Assidi , Adeel Chaudhary, Leena MerdadP51 Evaluation of the immunomodulatory effects of thymoquinone on human bone marrow mesenchymal stem cells (BM-MSCs) from osteoarthritic patientsSaadiah M Alfakeeh, Etimad A Alhwait, Mamdooh A Gari, Mohammed M Abbas, Mohammed H Alkaf, Haneen S Alsehli, Roaa Kadam, Gauthaman KalamegamP52 Implication of IL-10 and IL-28 polymorphism with successful anti-HCV therapy and viral clearanceRubi Ghazala, Shilu Mathew, M.Haroon Hamed, Mourad Assidi, Mohammed Al-Qahtani, Ishtiaq QadriP53 Selection of flavonoids against obesity protein (FTO) using in silico and in vitro approachesShilu Mathew, Lobna Mira, Manal Shaabad, Shireen Hussain, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-QahtaniP54 Computational selection and in vitro validation of flavonoids as new antidepressant agentsShilu Mathew, Manal Shaabad, Lobna Mira, Shireen Hussain, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-QahtaniP55 In Silico prediction and prioritization of aging candidate genes associated withprogressive telomere shorteningAhmed Rebai, Mourad Assidi, Abdelbaset Buhmeida, Muhammad Abu-Elmagd, Ashraf Dallol, Jerry W ShayP56 Identification of new cancer testis antigen genes in diverse types of malignant human tumour cellsMikhlid H AlmutairiP57 More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel sequencing (MPS)Angie Ambers, Jennifer Churchill, Jonathan King, Monika Stoljarova, Harrell Gill-King, Mourad Assidi, Muhammad Abu-Elmagd, Abdelbaset Buhmeida, Muhammad Al-Qatani, Bruce BudowleP58 Flow cytometry approach towards treatment men infertility in Saudi ArabiaMuhammad Abu-Elmagd, Farid Ahmed, Ashraf Dallol, Mourad Assidi, Taha Abo Almagd, Sahar Hakamy, Ashok Agarwal, Muhammad Al-Qahtani, Adel AbuzenadahP59 Tissue microarray based validation of CyclinD1 expression in renal cell carcinoma of Saudi kidney patientsSajjad Karim, Hans-Juergen Schulten, Ahmad J Al Sayyad, Hasan MA Farsi, Jaudah A Al-Maghrabi, Abdelbaset Buhmaida, Zeenat Mirza, Reem Alotibi, Alaa Al-Ahmadi, Nuha A Alansari, Alaa A Albogmi, Maha M Al-Quaiti, Fai T Ashgan, Afnan Bandah, Mohammed H Al-QahtaniP60 Assessment of gold nanoparticles in molecular diagnostics and DNA damage studiesRukhsana Satar, Mahmood Rasool, Waseem Ahmad, Nazia Nazam, Mohamad I Lone, Muhammad I Naseer, Mohammad S Jamal, Syed K Zaidi, Peter N Pushparaj, Mohammad A Jafri, Shakeel A Ansari, Mohammed H AlqahtaniP61 Surfing the biospecimen management and processing workflow at CEGMR BiobankHanan Bashier, Abrar Al Qahtani, Shilu Mathew, Amal M. Nour, Heba Alkhatabi, Adel M. Abu Zenadah, Abdelbaset Buhmeida, Mourad Assidi, Muhammed Al QahtaniP62 Autism Spectrum Disorder: knowledge, attitude and awareness in Jeddah, Kingdom of Saudi ArabiaMuhammad Faheem, Shilu Mathew, Shiny Mathew, Peter Natesan Pushparaj, Mohammad H. Al-QahtaniP63 Simultaneous genetic screening of the coagulation pathway genes using the Thromboscan targeted sequencing panelHani A. Alhadrami, Ashraf Dallol, Adel AbuzenadahP64 Genome wide array comparative genomic hybridization analysis in patients with syndromic congenital heart defectsIbtessam R. Hussein, Adeel G. Chaudhary, Rima S Bader, Randa Bassiouni, Maha Alquaiti, Fai Ashgan, Hans Schulten, Mohamed Nabil Alama, Mohammad H. Al QahtaniP65 Toxocogenetic evaluation of 1, 2-Dichloroethane in bone marrow, blood and cells of immune system using conventional, molecular and flowcytometric approachesMohammad I Lone, Nazia Nizam, Waseem Ahmad, Mohammad A Jafri, Mahmood Rasool, Shakeel A Ansari, Muhammed H Al-QahtaniP66 Molecular cytogenetic diagnosis of sexual development disorders in newborn: A case of ambiguous genitaliaEradah Alshihri, Muhammad Abu-Elmagd, Lina Alharbi, Mourad Assidi, Mohammed Al-QahtaniP67 Identification of disease specific gene expression clusters and pathways in hepatocellular carcinoma using In Silico methodologiesShilu Mathew, Peter Pushparaj Natesan, Muhammed Al QahtaniP68 Human Wharton’s Jelly stem cell conditioned medium inhibits primary ovarian cancer cells in vitro: Identification of probable targets and mechanisms using systems biologyGauthaman Kalamegam, Peter Natesan Pushparaj, Fazal Khan, Roaa Kadam, Farid Ahmed, Mourad Assidi, Khalid Hussain Wali Sait, Nisreen Anfinan, Mohammed Al QahtaniP69 Mutation spectrum of ASPM (Abnormal Spindle-like, Microcephaly-associated) gene in Saudi Arabian populationMuhammad I Naseer, Adeel G Chaudhary, Mohammad S Jamal, Shilu Mathew, Lobna S Mira, Peter N Pushparaj, Shakeel A Ansari, Mahmood Rasool, Mohammed H AlQahtaniP70 Identification and characterization of novel genes and mutations of primary microcephaly in Saudi Arabian populationMuhammad I Naseer, Adeel G Chaudhary, Shilu Mathew, Lobna S Mira, Mohammad S Jamal, Sameera Sogaty, Randa I Bassiouni, Mahmood Rasool, Mohammed H AlQahtaniP71 Molecular genetic analysis of hereditary nonpolyposis colorectal cancer (Lynch Syndrome) in Saudi Arabian populationMahmood Rasool, Shakeel A Ansari, Mohammad S Jamal, Peter N Pushparaj, Abdulrahman MS Sibiani, Waseem Ahmad, Abdelbaset Buhmeida, Mohammad A Jafri, Mohiuddin K Warsi, Muhammad I Naseer, Mohammed H Al-QahtaniP72 Function predication of hypothetical proteins from genome database of chlamydia trachomatisRubi, Kundan Kumar, Ahmad AT Naqvi, Faizan Ahmad, Md I Hassan, Mohammad S Jamal, Mahmood Rasool, Mohammed H AlQahtaniP73 Transcription factors as novel molecular targets for skin cancerAshraf Ali, Jummanah Jarullah, Mahmood Rasool, Abdelbasit Buhmeida, Shahida Khan, Ghufrana Abdussami, Maryam Mahfooz, Mohammad A Kamal, Ghazi A Damanhouri, Mohammad S JamalP74 An In Silico analysis of Plumbagin binding to apoptosis executioner: Caspase-3 and Caspase-7Bushra Jarullah, Jummanah Jarullah, Mohammad SS Jarullah, Ashraf Ali, Mahmood Rasool, Mohammad S JamalP75 Single cell genomics applications for preimplantation genetic screening optimization: Comparative analysis of whole genome amplification technologiesMourad Assidi, Muhammad Abu-Elmagd, Osama Bajouh, Peter Natesan Pushparaj, Mohammed Al-Qahtani, Adel AbuzenadahP76 ZFP36 regulates miRs-34a in anti-IgM triggered immature B cellsMohammad S Jamal, Jummanah Jarullah, Abdulah EA Mathkoor, Hashim MA Alsalmi, Anas MM Oun, Ghazi A Damanhauri, Mahmood Rasool, Mohammed H AlQahtaniP77 Identification of a novel mutation in the STAMBP gene in a family with microcephaly-capillary malformation syndromeMuhammad I. Naseer, Mahmood Rasool, Sameera Sogaty, Adeel G. Chudhary, Yousif A. Abutalib, Daniele Merico, Susan Walker, Christian R. Marshall, Mehdi Zarrei, Stephen W. Scherer, Mohammad H. Al-QahtaniP78 Copy number variations in Saudi patients with intellectual disability and epilepsyMuhammad I. Naseer, Muhammad Faheem, Adeel G. Chaudhary, Mahmood Rasool, Gauthaman Kalamegam, Fai Talal Ashgan, Mourad Assidi, Farid Ahmed, Syed Kashif Zaidi, Mohammed M. Jan, Mohammad H. Al-QahtaniP79 Prognostic significance of CD44 expression profile in colorectal carcinomaMaryam Al-Zahrani, Sahira Lary, Sahar Hakamy, Ashraf Dallol, Mahmoud Al-Ahwal, Jaudah Al-Maghrabi, Emmanuel Dermitzakis, Adel Abuzenadah, Abdelbaset Buhmeida, Mohammed Al-QahtaniP80 Association of the endothelial nitric oxide synthase (eNOS) gene G894T polymorphism with hypertension risk and complicationsAbeer A Al-refai, Mona Saleh, Rehab I Yassien, Mahmmoud Kamel, Rabab M HabebP81 SNPs array to screen genetic variation among diabetic patientsNajlaa Filimban, Ashraf Dallol, Nadia Ghannam, Mohammed Al-Qahtani, Adel Mohammed AbuzenadahP82 Detection and genotyping of Helicobacter pylori among gastric cancer patients from Saudi Arabian populationFehmida Bibi, Sana Akhtar, Esam I. Azhar, Muhammad Yasir, Muhammad I. Nasser, Asif A. Jiman-Fatani, Ali SawanP83 Antimicrobial drug resistance and molecular detection of susceptibility to Fluoroquinolones among clinical isolates of Salmonella species from Jeddah-Saudi ArabiaRuaa A Lahzah, Asho AliP84 Identification of the toxic and virulence nature of MAP1138c protein of Mycobacterium avium subsp. paratuberculosisSyed A Hassan, Seyed E Hasnain, Iftikhar A Tayubi, Hamza A Abujabal, Alaa O MagrabiP85 In vitro and in silico evaluation of miR137 in human breast cancerFazal Khan, Gauthaman Kalamegam, Peter Natesan Pushparaj, Adel Abuzenada, Taha Abduallah Kumosani, Elie Barbour, Mohammed Al-QahtaniP86 Auruka gene is over-expressed in Saudi breast cancerManal Shabaad, Shilu Mathew, Ashraf Dallol, Adnan Merdad, Abdelbaset Buhmeida, Mohammed Al-QahtaniP87 The potential of immunogenomics in personalized healthcareMourad Assidi, Muhammad Abu-Elmagd, Kalamegam Gauthaman, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Peter Natesan Pushparaj, Mohammed Al-QahtaniP88 In Silico physiochemical and structural characterization of a putative ORF MAP0591 and its implication in the pathogenesis of Mycobacterium paratuberculosis in ruminants and humansSyed A Hassan, Iftikhar A Tayubi, Hani MA AljahdaliP89 Effects of heat shock on human bone marrow mesenchymal stem cells (BM-MSCs): Implications in regenerative medicineReham Al Nono, Mamdooh Gari, Haneen Alsehli, Farid Ahmed, Mohammed Abbas, Gauthaman Kalamegam, Mohammed Al-QahtaniP90 In Silico analyses of the molecular targets of Resveratrol unravels its importance in mast cell mediated allergic responsesShilu Mathew, Fazal Khan, Mahmood Rasool, Mohammed Sarwar Jamal, Muhammad Imran Naseer, Zeenat Mirza, Sajjad Karim, Shakeel Ansari, Mourad Assidi, Gauthaman Kalamegam, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Peter Natesan Pushparaj, Mohammed Al-QahtaniP91 Effects of environmental particulate matter on bone-marrow mesenchymal stem cellsMuhammad Abu-Elmagd, Gauthaman Kalamegam, Roaa Kadam, Mansour A Alghamdi, Magdy Shamy, Max Costa, Mamdouh I Khoder, Mourad Assidi, Peter Natesan Pushparaj, Mamdooh Gari, Mohammed Al-QahtaniP92 Distinctive charge clusters in human virus proteomesNajla Kharrat, Sabrine Belmabrouk, Rania Abdelhedi, Riadh Benmarzoug, Mourad Assidi, Mohammed H. Al Qahtani, Ahmed RebaiP93 In vitro experimental model and approach in identification of new biomarkers of inflammatory forms of arthritisGhazi Dhamanhouri, Peter Natesan Pushparaj, Abdelwahab Noorwali, Mohammad Khalid Alwasiyah, Afnan Bahamaid, Saadiah Alfakeeh, Aisha Alyamani, Haneen Alsehli, Mohammed Abbas, Mamdooh Gari, Ali Mobasheri, Gauthaman Kalamegam, Mohammed Al-QahtaniP94 Molecular docking of GABAA receptor subunit γ-2 with novel anti-epileptic compoundsMuhammad Faheem, Shilu Mathew, Peter Natesan Pushparaj, Mohammad H. Al-QahtaniP95 Breast cancer knowledge, awareness, and practices among Saudi females residing in JeddahShilu Mathew, Muhammad Faheem, Shiny Mathew, Peter Natesan Pushparaj, Mohammad H. Al-QahtaniP96 Anti-inflammatory role of Sesamin by Attenuation of Iba1/TNF-α/ICAM-1/iNOS signaling in Diabetic RetinopathyMohammad Sarwar Jamal, Syed Kashif Zaidi, Raziuddin Khan, Kanchan Bhatia, Mohammed H. Al-Qahtani, Saif AhmadP97 Identification of drug lead molecule against vp35 protein of Ebola virus: An In-Silico approachIftikhar AslamTayubi, Manish Tripathi, Syed Asif Hassan, Rahul ShrivastavaP98 An approach to personalized medicine from SNP-calling through disease analysis using whole exome-sequencing of three sub-continental populationsIftikhar A Tayubi, Syed Hassan, Hamza A.S AbujabalP99 Low versus high frequency of Glucose –6 – Phosphate Dehydrogenase (G6PD) deficiency in urban against tribal population of Gujarat – A signal to natural selectionIshani Shah, Bushra Jarullah, Mohammad S Jamal, Jummanah JarullahP100 Spontaneous preterm birth and single nucleotide gene polymorphisms: a recent updateIshfaq A Sheikh, Ejaz Ahmad, Mohammad S Jamal, Mohd Rehan, Muhammad Abu-Elmagd, Iftikhar A Tayubi, Samera F AlBasri, Osama S Bajouh, Rola F Turki, Adel M Abuzenadah, Ghazi A Damanhouri, Mohd A Beg, Mohammed Al-QahtaniP101 Prevalence of congenital heart diseases among Down syndrome cases in Saudi Arabia: role of molecular genetics in the pathogenesisSahar AF Hammoudah, Khalid M AlHarbi, Lama M El-Attar, Ahmed MZ DarwishP102 Combinatorial efficacy of specific pathway inhibitors in breast cancer cellsSara M Ibrahim, Ashraf Dallol, Hani Choudhry, Adel Abuzenadah, Jalaludden Awlia, Adeel Chaudhary, Farid Ahmed, Mohammed Al-QahtaniP103 MiR-143 and miR-145 cluster as potential replacement medicine for the treatment of cancerMohammad A Jafri, Muhammad Abu-Elmagd, Mourad Assidi, Mohammed Al-QahtaniP104 Metagenomic profile of gut microbiota during pregnancy in Saudi populationImran khan, Muhammad Yasir, Esam I. Azhar, Sameera Al-basri, Elie Barbour, Taha KumosaniP105 Exploration of anticancer targets of selected metabolites of Phoenix dactylifera L. using systems biological approachesFazal Khan, Gauthaman Kalamegam, Peter Natesan Pushparaj, Adel Abuzenada, Taha Abduallah Kumosani, Elie BarbourP106 CD226 and CD40 gene polymorphism in susceptibility to Juvenile rheumatoid arthritis in Egyptian patientsHeba M. EL Sayed, Eman A. HafezP107 Paediatric exome sequencing in autism spectrum disorder ascertained in Saudi familiesHans-Juergen Schulten, Aisha Hassan Elaimi, Ibtessam R Hussein, Randa Ibrahim Bassiouni, Mohammad Khalid Alwasiyah, Richard F Wintle, Adeel Chaudhary, Stephen W Scherer, Mohammed Al-QahtaniP108 Crystal structure of the complex formed between Phospholipase A2 and the central core hydrophobic fragment of Alzheimer’s β- amyloid peptide: a reductionist approachZeenat Mirza, Vikram Gopalakrishna Pillai, Sajjad Karim, Sujata Sharma, Punit Kaur, Alagiri Srinivasan, Tej P Singh, Mohammed Al-QahtaniP109 Differential expression profiling between meningiomas from female and male patientsReem Alotibi, Alaa Al-Ahmadi, Fatima Al-Adwani, Deema Hussein, Sajjad Karim, Mona Al-Sharif, Awatif Jamal, Fahad Al-Ghamdi, Jaudah Al-Maghrabi, Saleh S Baeesa, Mohammed Bangash, Adeel Chaudhary, Hans-Juergen Schulten, Mohammed Al-QahtaniP110 Neurospheres as models of early brain development and therapeuticsMuhammad Faheem, Peter Natesan Pushparaj, Shilu Mathew, Taha Abdullah Kumosani, Gauthaman Kalamegam, Mohammed Al-QahtaniP111 Identification of a recurrent causative missense mutation p.(W577C) at the LDLR exon 12 in familial hypercholesterolemia affected Saudi familiesFaisal A Al-Allaf, Zainularifeen Abduljaleel, Abdullah Alashwal, Mohiuddin M. Taher, Abdellatif Bouazzaoui, Halah Abalkhail, Faisal A. Ba-Hammam, Mohammad AtharP112 Epithelial ovarian carcinoma (EOC): Systems oncological approach to identify diagnostic, prognostic and therapeutic biomarkersGauthaman Kalamegam, Peter Natesan Pushparaj, Muhammad Abu-Elmagd, Farid Ahmed Khalid HussainWali Sait, Nisreen Anfinan, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Mourad Assidi, Mohammed Al-QahtaniP113 Crohn’s disease phenotype in northern Tunisian populationNaira Ben Mami, Yosr Z Haffani, Mouna Medhioub, Lamine Hamzaoui, Ameur Cherif, Msadok AzouzP114 Establishment of In Silico approaches to decipher the potential toxicity and mechanism of action of drug candidates and environmental agentsGauthaman Kalamegam, Fazal Khan, Shilu Mathew, Mohammed Imran Nasser, Mahmood Rasool, Farid Ahmed, Peter Natesan Pushparaj, Mohammed Al-QahtaniP115 1q Gain predicts poor prognosis marker for young breast cancer patientsShereen A Turkistany, Lina M Al-harbi, Ashraf Dallol, Jamal Sabir, Adeel Chaudhary, Adel AbuzenadahP116 Disorders of sex chromosomes in a diagnostic genomic medicine unit in Saudi Arabia: Prevalence, diagnosis and future guidelinesBasmah Al-Madoudi, Bayan Al-Aslani, Khulud Al-Harbi, Rwan Al-Jahdali, Hanadi Qudaih, Emad Al Hamzy, Mourad Assidi, Mohammed Al QahtaniP117 Combination of WYE354 and Sunitinib demonstrate synergistic inhibition of acute myeloid leukemia in vitroAsad M Ilyas, Youssri Ahmed, Mamdooh Gari, Farid Ahmed, Mohammed AlqahtaniP118 Integrated use of evolutionary information in GWAS reveals important SNPs in AsthmaNada Salem, Sajjad Karim, Elham M Alhathli, Heba Abusamra, Hend F Nour Eldin, Mohammed H Al-Qahtani, Sudhir KumarP119 Assessment of BRAF, IDH1, IDH2, and EGFR mutations in a series of primary brain tumorsFatima Al-Adwani, Deema Hussein, Mona Al-Sharif, Awatif Jamal, Fahad Al-Ghamdi, Jaudah Al-Maghrabi, Saleh S Baeesa, Mohammed Bangash, Adeel Chaudhary, Mohammed Al-Qahtani, Hans-Juergen SchultenP120 Expression profiles distinguish oligodendrogliomas from glioblastoma multiformes with or without oligodendroglioma componentAlaa Alamandi, Reem Alotibi, Deema Hussein, Sajjad Karim, Jaudah Al-Maghrabi, Fahad Al-Ghamdi, Awatif Jamal, Saleh S Baeesa, Mohammed Bangash, Adeel Chaudhary, Hans-Juergen Schulten, Mohammed Al-QahtaniP121 Hierarchical clustering in thyroid goiters and hyperplastic lesionsOhoud Subhi, Nadia Bagatian, Sajjad Karim, Adel Al-Johari, Osman Abdel Al-Hamour, Hosam Al-Aradati, Abdulmonem Al-Mutawa, Faisal Al-Mashat, Jaudah Al-Maghrabi, Hans-Juergen Schulten, Mohammad Al-QahtaniP122 Differential expression analysis in thyroiditis and papillary thyroid carcinomas with or without coexisting thyroiditisNadia Bagatian, Ohoud Subhi, Sajjad Karim, Adel Al-Johari, Osman Abdel Al-Hamour, Abdulmonem Al-Mutawa, Hosam Al-Aradati, Faisal Al-Mashat, Mohammad Al-Qahtani, Hans-Juergen Schulten, Jaudah Al-MaghrabiP123 Metagenomic analysis of waste water microbiome in Sausdi ArabiaMuhammad W shah, Muhammad Yasir, Esam I Azhar, Saad Al-MasoodiP124 Molecular characterization of Helicobacter pylori from faecal samples of Tunisian patients with gastric cancerYosr Z Haffani, Msadok Azouz, Emna Khamla, Chaima Jlassi, Ahmed S. Masmoudi, Ameur Cherif, Lassaad BelbahriP125 Diagnostic application of the oncoscan© panel for the identification of hereditary cancer syndromeShadi Al-Khayyat, Roba Attas, Atlal Abu-Sanad, Mohammed Abuzinadah, Adnan MerdadAshraf Dallol, Adeel Chaudhary, Mohammed Al-Qahtani, Adel AbuzenadahP126 Characterization of clinical and neurocognitive features in a family with a novel OGT gene missense mutation c. 1193G > A/ (p. Ala319Thr)Habib Bouazzi, Carlos Trujillo, Mohammad Khalid Alwasiyah, Mohammed Al-QahtaniP127 Case report: a rare homozygous deletion mutation of TMEM70 gene associated with 3-Methylglutaconic Aciduria and cataract in a Saudi patientMaha Alotaibi, Rami NassirP128 Isolation and purification of antimicrobial milk proteinsIshfaq A Sheikh, Mohammad A Kamal, Essam H Jiffri, Ghulam M Ashraf, Mohd A BegP129 Integrated analysis reveals association of ATP8B1 gene with colorectal cancerMohammad A Aziz, Rizwan Ali, Mahmood Rasool, Mohammad S Jamal, Nusaibah samman, Ghufrana Abdussami, Sathish Periyasamy, Mohiuddin K Warsi, Mohammed Aldress, Majed Al Otaibi, Zeyad Al Yousef, Mohamed Boudjelal, Abdelbasit Buhmeida, Mohammed H Al-Qahtani, Ibrahim AlAbdulkarimP130 Implication of IL-10 and IL-28 polymorphism with successful anti-HCV therapy and viral clearanceRubi Ghazala, Shilu Mathew, M. Haroon Hamed, Mourad Assidi, Mohammed Al-Qahtani, Ishtiaq QadriP131 Interactions of endocrine disruptor di-(2-ethylhexyl) phthalate (DEHP) and its metabolite mono-2-ethylhexyl phthalate (MEHP) with progesterone receptorIshfaq A Sheikh, Muhammad Abu-Elmagd, Rola F Turki, Ghazi A Damanhouri, Mohd A. BegP132 Association of HCV nucleotide polymorphism in the development of hepatocellular carcinomaMohd Suhail, Abid Qureshi, Adil Jamal, Peter Natesan Pushparaj, Mohammad Al-Qahtani, Ishtiaq QadriP133 Gene expression profiling by DNA microarrays in colon cancer treated with chelidonine alkaloidMahmoud Z El-Readi, Safaa Y Eid, Michael WinkP134 Successful in vitro fertilization after eight failed trialsAhmed M. Isa, Lulu Alnuaim, Johara Almutawa, Basim Abu-Rafae, Saleh Alasiri, Saleh BinsalehP135 Genetic sensitivity analysis using SCGE, cell cycle and mitochondrial membrane potential in OPs stressed leukocytes in Rattus norvegicus through flow cytometric inputNazia Nazam, Mohamad I Lone, Waseem Ahmad, Shakeel A Ansari, Mohamed H Alqahtani

BackgroundWe have generated a series of isogenically derived immortalized human colonic epithelial cell (HCEC 1CT and HCEC 2CT) lines, including parental un-immortalized normal cell strains. The CDK4 and hTERT immortalized colonic epithelial cell line (HCEC 1CT) is initially karyotypically normal diploid and expresses a series of epithelial cell markers including stem cell markers. Under stressful tissue culture conditions, a spontaneous aneuploidy event occurred in the HCEC 1CT line, resulting in a single chromosomal change leading to a stable trisomy 7 cell line (1CT7). Trisomy 7 occurs in about 40% of all benign human adenomas (polyps) and thus this specific chromosomal change in diploid HCEC 1CT cells appears to be non random. In addition, we have partially transformed the HCEC 1CT line by introducing stable knockdown of wild type APC and TP53, and ectopically introducing a mutant Krasv12 and a mutant version of APC (A1309), all commonly found mutations in colorectal cancer (CRC).MethodsWhole exome sequencing and bioinformatic analyses were performed to comprehensively examine the genetic background of these isogenic cell lines.ResultsExome sequencing of these experimentally progressed cell lines recapitulates a list of genes previously reported to be involved in CRC tumorigenesis. In addition, sequencing revealed a collection of novel genes specifically detected in 1CT7 and A1309 cells but not normal diploid 1CT cells.ConclusionThis study demonstrates the utility of using isogenic experimentally derived HCEC lines as a model to recapitulate CRC initiation and progression. Exome sequencing reveals a collection of novel genes that may play important roles in CRC tumorigenesis.

BackgroundBreast cancer incidence rates are increasing at an alarming rate among Saudi Arabian females. Most molecular genetic discoveries on breast cancer and other cancers have arisen from studies examining European and American patients. However, possibility of specific changes in molecular signature among cancer patients of diverse ethnic groups remains largely unexplored. We performed transcriptomic profiling of surgically-resected breast tumors from 45 patients based in the Western region of Saudi Arabia using Affymetrix Gene 1.0 ST chip. Pathway and biological function-based clustering was apparent across the tissue samples.ResultsPathway analysis revealed canonical pathways that had not been previously implicated in breast cancer. Biological network analysis of differentially regulated genes revealed that Fatty acid binding protein 4, adipocyte (FABP4), adiponectin (ADIPOQ), and retinol binding protein 4 (RBP4) were most down regulated genes, sharing strong connection with the other molecules of lipid metabolism pathway. The marked biological difference in the signatures uncovered between the USA and Saudi samples underpins the importance of this study. Connectivity Map identified compounds that could reverse an observed gene expression signatureConclusionsThis study describes, to our knowledge, the first genome-wide profiling of breast cancer from Saudi ethnic females. We demonstrate the involvement of the lipid metabolism pathway in the pathogenesis of breast cancer from this region. This finding also highlights the need for strategies to curb the increasing rates of incidence of this disease by educating the public about life-style risk factors such as unhealthy diet and obesity.