Global genetic variation of select opiate metabolism genes in self-reported healthy individuals

CYP2D6 is a key pharmacogene encoding an enzyme impacting poor, intermediate, extensive and ultrarapid phase I metabolism of many marketed drugs. The pharmacogenetics of opiate drug metabolism is particularly interesting due to the relatively high incidence of addiction and overdose. Recently, trans-acting opiate metabolism and analgesic response enzymes (UGT2B7, ABCB1, OPRM1 and COMT) have been incorporated into pharmacogenetic studies to generate more comprehensive metabolic profiles of patients. With use of massively parallel sequencing, it is possible to identify additional polymorphisms that fine tune, or redefine, previous pharmacogenetic findings, which typically rely on targeted approaches. The 1000 Genomes Project data were analyzed to describe population genetic variation and statistics for these five genes in self-reported healthy individuals in five global super- and 26 sub-populations. Findings on the variation of these genes in various populations expand baseline understanding of pharmacogenetically relevant polymorphisms for future studies of affected cohorts.

STRait Razor v2s: Advancing sequence-based STR allele reporting and beyond to other marker systems

STRait Razor has provided the forensic community a free-to-use, open-source tool for short tandem repeat (STR) analysis of massively parallel sequencing (MPS) data. STRait Razor v2s (SRv2s) allows users to capture physically phased haplotypes within the full amplicon of both commercial (ForenSeq) and "early access" panels (PowerSeq, Mixture ID). STRait Razor v2s may be run in batch mode to facilitate population-level analysis and is supported by all Unix distributions (including MAC OS). Data are reported in tables in string (haplotype), length-based (e.g., vWA allele 14), and International Society of Forensic Genetics (ISFG)-recommended (vWA [CE 14]-GRCh38-chr12:5983950-5984049 (TAGA)₁₀ (CAGA)₃ TAGA) formats. STRait Razor v2s currently contains a database of ∼2500 unique sequences. This database is used by SRv2s to match strings to the appropriate allele in ISFG-recommended format. In addition to STRs, SRv2s has configuration files necessary to capture and report haplotypes from all marker types included in these multiplexes (e.g., SNPs, InDels, and microhaplotypes). To facilitate mixture interpretation, data may be displayed from all markers in a format similar to that of electropherograms displayed by traditional forensic software. The download package for SRv2s may be found at https://www.unthsc.edu/graduate-school-of-biomedical-sciences/molecular-and-medical-genetics/laboratory-faculty-and-staff/strait-razor.

The factor of 10 in forensic DNA match probabilities

An update was performed of the classic experiments that led to the view that profile probability assignments are usually within a factor of 10 of each other. The data used in this study consist of 15 Identifiler loci collected from a wide range of forensic populations. Following Budowle et al. [1], the terms cognate and non-cognate are used. The cognate database is the database from which the profiles are simulated. The profile probability assignment was usually larger in the cognate database. In 44%-65% of the cases, the profile probability for 15 loci in the non-cognate database was within a factor of 10 of the profile probability in the cognate database. This proportion was between 60% and 80% when the FBI and NIST data were used as the non-cognate databases. A second experiment compared the match probability assignment using a generalised database and recommendation 4.2 from NRC II (the 4.2 assignment) with a proxy for the matching proportion developed using subpopulation allele frequencies and the product rule. The findings support that the 4.2 assignment has a large conservative bias. These results are in agreement with previous research results.

General Aviation Pilots Over 70 Years Old

BACKGROUND

Currently it is not unusual for general aviation pilots in the United States to continue to fly beyond the age of 70, even into their 80s and 90s. Pilots have regular examinations according to protocols which do not specify special or additional requirements for pilots over 70 yr of age. Additionally, the third class medical reforms passed by the U.S. Senate on 15 July 2016 could potentially result in even less stringent medical certification requirements for general aviation pilots.

METHODS

Accident rates, medical parameters, autopsy findings, and toxicological findings from the U.S. National Transportation Safety Board (NTSB) general aviation (GA) accident database were analyzed to assess potential risk factors with accident outcomes.

RESULTS

During 2003-2012, there were 114 (113 men, 1 woman) general aviation fatal accidents involving pilots ages 70 to 92 yr. A combination of 3 or more drugs were found in 13 (13%) of deceased pilots. The most frequent drugs were first generation antihistamines and antidepressants represented the next highest proportion of possible performance-affecting medications.

CONCLUSION

This study indicates that there are critical medical factors that may contribute to fatal accidents among elderly pilots. Polypharmacy use should be taken into consideration, especially during periodic health examinations and fatal aviation investigations involving elderly pilots.Vuorio A, Asmayawati S, Budowle B, Griffiths R, Strandberg T, Kuoppala J, Sajantila A. General aviation pilots over 70 years old. Aerosp Med Hum Perform. 2017; 88(2):142-145.

Bipolar Disorder in Aviation Medicine

BACKGROUND

One of the most difficult challenges in aviation medicine is to diagnose, as early as possible, pilots with psychiatric disorders that may impair pilot performance and increase the risk of incidents and accidents. This diagnosis applies particularly to bipolar disorder (BD), where return to flying duty is not an option in the majority of cases. BD is a long-term mental disorder presenting remittent depressive, hypomanic, manic, or mixed episodes between low symptomatic or asymptomatic intermediate periods. Onset in most cases is in late teen or early adult years. Suicidal intentions and suicide risk are significantly elevated in individuals with BD compared to the general population.

METHODS

A systematic literature search was performed of BD and aviation accidents and the National Transportation Safety Board database of fatal general aviation accidents was searched. One case report and two database reports of interest from 1994 to 2014 were identified.

RESULTS

The findings set a minimum frequency of BD in general aviation fatalities to be approximately 2 out of 8648 (0.023%) in the United States.

DISCUSSION

The reported incidence may underestimate the real number of BD cases for several reasons, including the fact that the medical history of pilots is not always available or is sometimes not the primary interest of a safety investigation. This study suggests that the demarcation of psychiatric disorder related to fitness to fly is an important step in safety.Vuorio A, Laukkala T, Navathe P, Budowle B, Bor R, Sajantila A. Bipolar disorder in aviation medicine. Aerosp Med Hum Perform. 2017; 88(1):42-47.

A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes

Single source and multiple donor (mixed) samples of human mitochondrial DNA were analyzed and compared using the MinION and the MiSeq platforms. A generalized variant detection strategy was employed to provide a cursory framework for evaluating the reliability and accuracy of mitochondrial sequences produced by the MinION. The feasibility of long-read phasing was investigated to establish its efficacy in quantitatively distinguishing and deconvolving individuals in a mixture. Finally, a proof-of-concept was demonstrated by integrating both platforms in a hybrid assembly that leverages solely mixture data to accurately reconstruct full mitochondrial genomes.

The genetic structure of native Americans in North America based on the Globalfiler® STRs

Current forensic STR databases, such as CODIS, lack population genetic data on Native American populations. Information from a geographically diverse array of tribes is necessary to provide improved statistical estimates of the strength of associations with DNA evidence. The Globalfiler® STR markers were used to characterize the genetic structure of ten tribal populations from seven geographic regions in North America, including those not presently represented in forensic databases. Samples from the Arctic region, Baja California, California/Great Basin, the Southeast, Mexico, the Midwest, and the Southwest were analyzed for allele frequencies, observed and expected heterozygosities, and F-statistics. The tribal samples exhibited an F_ST or θ value above the conservative 0.03 estimate recommended by the National Research Council (NRC) for calculating random match probabilities among Native Americans. The greater differentiation among tribal populations computed here (θ=0.04) warrants the inclusion of additional regional Native American samples into STR databases.

Paternity calculations in a di-spermy case

In a criminal paternity case, which involved analysis of the product of conception, a rare circumstance was observed. The product of conception was triploidy, apparently due to an egg fertilized by two sperm. Since there is little guidance on how to calculate the probability of the DNA evidence given some basic hypotheses, the formulae were derived and are presented herein. These approaches could provide guidance for similar situations if they arise.

More comprehensive forensic genetic marker analyses for accurate human remains identification using massively parallel DNA sequencing

BACKGROUND

Although the primary objective of forensic DNA analyses of unidentified human remains is positive identification, cases involving historical or archaeological skeletal remains often lack reference samples for comparison. Massively parallel sequencing (MPS) offers an opportunity to provide biometric data in such cases, and these cases provide valuable data on the feasibility of applying MPS for characterization of modern forensic casework samples. In this study, MPS was used to characterize 140-year-old human skeletal remains discovered at a historical site in Deadwood, South Dakota, United States. The remains were in an unmarked grave and there were no records or other metadata available regarding the identity of the individual. Due to the high throughput of MPS, a variety of biometric markers could be typed using a single sample.

RESULTS

Using MPS and suitable forensic genetic markers, more relevant information could be obtained from a limited quantity and quality sample. Results were obtained for 25/26 Y-STRs, 34/34 Y SNPs, 166/166 ancestry-informative SNPs, 24/24 phenotype-informative SNPs, 102/102 human identity SNPs, 27/29 autosomal STRs (plus amelogenin), and 4/8 X-STRs (as well as ten regions of mtDNA). The Y-chromosome (Y-STR, Y-SNP) and mtDNA profiles of the unidentified skeletal remains are consistent with the R1b and H1 haplogroups, respectively. Both of these haplogroups are the most common haplogroups in Western Europe. Ancestry-informative SNP analysis also supported European ancestry. The genetic results are consistent with anthropological findings that the remains belong to a male of European ancestry (Caucasian). Phenotype-informative SNP data provided strong support that the individual had light red hair and brown eyes.

CONCLUSIONS

This study is among the first to genetically characterize historical human remains with forensic genetic marker kits specifically designed for MPS. The outcome demonstrates that substantially more genetic information can be obtained from the same initial quantities of DNA as that of current CE-based analyses.

The Third International Genomic Medicine Conference (3rd IGMC, 2015): overall activities and outcome highlights

The Third International Genomic Medicine Conference (3^rd 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 (1^st IGMC, 2011) followed by the second International Genomic Medicine Conference (2^nd IGMC, 2013). The 3^rd 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.

Enhancement of Pathologist's Routine Practice: Reuse of DNA Extracted from Immunostained Formalin-fixed Paraffin-embedded (FFPE) Slides in Downstream Molecular Analysis of Cancer

BACKGROUND/AIM

To date, the conventional formalin-fixed, paraffin-embedded (FFPE) technique is the gold-standard for preserving histomorphology. Once FFPE tissues are stained, slides are routinely archived along with their blocks at biobanks/hospitals. However, the reuse of fixed and stained biospecimens as DNA source is not a common routine practice worldwide and, thus, indicates the need of studies to investigate the feasibility of extracting DNA from already immunohistochemistry (IHC) FFPE-stained slides and its possible reuse in subsequent downstream molecular analyses.

MATERIALS AND METHODS

FFPE IHC slides from colorectal cancer (CRC) patients were prepared and stored in the CEGMR Biobank. The workflow consists of digitalization of IHC stained slide's image, removing the slide cover-slip, crude dissection and DNA extraction. Following DNA quality assessment, mutation analysis of CTNNB1 and methylation profile of CDH1 were performed.

RESULTS

High-quality DNA was obtained allowing 60% concordance between CDH1 methylation and membranous E-cadherin expression pattern. Clean CTNNB1 DNA chromatograms with evenly-spaced peaks were observed.

CONCLUSION

This study is a proof of concept to recycle and reuse DNA from IHC stained slides with suitable concentration and integrity for further downstream molecular applications. These findings will enhance the pathologists' knowledge, attitudes and practices (KAP) towards the use of these biospecimens and support the implementation of this approach in clinical pathology practice. Therefore, the scientific community will benefit from the largest comprehensive database of human fully annotated FFPE biospecimens already available at their disposal in order to demystify the complexity and the heterogeneity of many challenging diseases and foster the transition towards precision medicine.

Evaluation of forensic DNA mixture evidence: protocol for evaluation, interpretation, and statistical calculations using the combined probability of inclusion

Background

The evaluation and interpretation of forensic DNA mixture evidence faces greater interpretational challenges due to increasingly complex mixture evidence. Such challenges include: casework involving low quantity or degraded evidence leading to allele and locus dropout; allele sharing of contributors leading to allele stacking; and differentiation of PCR stutter artifacts from true alleles. There is variation in statistical approaches used to evaluate the strength of the evidence when inclusion of a specific known individual(s) is determined, and the approaches used must be supportable. There are concerns that methods utilized for interpretation of complex forensic DNA mixtures may not be implemented properly in some casework. Similar questions are being raised in a number of U.S. jurisdictions, leading to some confusion about mixture interpretation for current and previous casework.

Results

Key elements necessary for the interpretation and statistical evaluation of forensic DNA mixtures are described. Given the most common method for statistical evaluation of DNA mixtures in many parts of the world, including the USA, is the Combined Probability of Inclusion/Exclusion (CPI/CPE). Exposition and elucidation of this method and a protocol for use is the focus of this article. Formulae and other supporting materials are provided.

Conclusions

Guidance and details of a DNA mixture interpretation protocol is provided for application of the CPI/CPE method in the analysis of more complex forensic DNA mixtures. This description, in turn, should help reduce the variability of interpretation with application of this methodology and thereby improve the quality of DNA mixture interpretation throughout the forensic community.

Electronic supplementary material

The online version of this article (doi:10.1186/s12863-016-0429-7) contains supplementary material, which is available to authorized users.

Expansion of Microbial Forensics

Microbial forensics has been defined as the discipline of applying scientific methods to the analysis of evidence related to bioterrorism, biocrimes, hoaxes, or the accidental release of a biological agent or toxin for attribution purposes. Over the past 15 years, technology, particularly massively parallel sequencing, and bioinformatics advances now allow the characterization of microorganisms for a variety of human forensic applications, such as human identification, body fluid characterization, postmortem interval estimation, and biocrimes involving tracking of infectious agents. Thus, microbial forensics should be more broadly described as the discipline of applying scientific methods to the analysis of microbial evidence in criminal and civil cases for investigative purposes.

K, Aldahlawi AM, Saadah O, McCoy JP, El-Tarras AE, Awad NS, Alharthi AA, Ibrahim MMM, Alsehli HS, Dallol A, Gari AM, Abbas MM, Kadam RA, Gari MM, Alkaff MH, Abuzenadah AM, Gari MA, Abusamra H, Karim S, eldin HFN, Alhathli EM, Salem N, Kumar S, Al-Qahtani MH, Moradi FA, Rashidi OM, Awan ZA, Kaya IH, Al-Harazi O, Colak D, Alkousi NA, Athanasopoulos T, Bahmaid AO, Alhwait EA, Gari MA, Alsehli HS, Abbas MM, Alkaf MH, Kadam R, Dallol A, Kalamegam G, Eldin HFN, Karim S, Abusamra H, Alhathli E, Salem N, Al-Qahtani MH, Kumar S, Alsayed SN, Aljohani FH, Habeeb SM, Almashali RA, Basit S, Ahmed SM, Sharma R, Agarwal A, Durairajanayagam D, Samanta L, Abu-Elmagd M, Abuzenadah AM, Sabanegh ES, Assidi M, Al-Qahtani M, Agarwal A, Sharma R, Samanta L, Durairajanayagam D, Assidi M, Abu-Elmagd M, Al-Qahtani M, Abuzenadah AM, Sabanegh ES, Samanta L, Agarwal A, Sharma R, Cui Z, Assidi M, Abuzenadah AM, Abu-Elmagd M, Al-Qahtani M, Alboogmi AA, Alansari NA, Al-Quaiti MM, Ashgan FT, Bandah A, Jamal HS, Rozi A, Mirza Z, Abuzenadah AM, Karim S, Al-Qahtani MH, Karim S, Schulten HJ, Al Sayyad AJ, Farsi HMA, Al-Maghrabi JA, Mirza Z, Alotibi R, Al-Ahmadi A, Alansari NA, Albogmi AA, Al-Quaiti MM, Ashgan FT, Bandah A, Al-Qahtani MH, Ebiya RA, Darwish SM, Montaser MM, Abusamra H, Bajic VB, Al-Maghrabi J, Gomaa W, Hanbazazh M, Al-Ahwal M, Al-Harbi A, Al-Qahtani W, Hakamy S, Baba G, Buhmeida A, Al-Qahtani M, Al-Maghrabi J, Al-Harbi A, Al-Ahwal M, Al-Harbi A, Al-Qahtani W, Hakamy S, Baba G, Buhmeida A, Al-Qahtani M, Alhathli EM, Karim S, Salem N, Eldin HN, Abusamra H, Kumar S, Al-Qahtani MH, Alyamani AA, Kalamegam G, Alhwait EA, Gari MA, Abbas MM, Alkaf MH, Alsehli HS, Kadam RA, Al-Qahtani M, Gadi R, Buhmeida A, Assidi M, Chaudhary A, Merdad L, Alfakeeh SM, Alhwait EA, Gari MA, Abbas MM, Alkaf MH, Alsehli HS, Kadam R, Kalamegam G, Ghazala R, Mathew S, Hamed MH, Assidi M, Al-Qahtani M, Qadri I, Mathew S, Mira L, Shaabad M, Hussain S, Assidi M, Abu-Elmagd M, Al-Qahtani M, Mathew S, Shaabad M, Mira L, Hussain S, Assidi M, Abu-Elmagd M, Al-Qahtani M, Rebai A, Assidi M, Buhmeida A, Abu-Elmagd M, Dallol A, Shay JW, Almutairi MH, Ambers A, Churchill J, King J, Stoljarova M, Gill-King H, Assidi M, Abu-Elmagd M, Buhmeida A, Al-Qatani M, Budowle B, Abu-Elmagd M, Ahmed F, Dallol A, Assidi M, Almagd TA, Hakamy S, Agarwal A, Al-Qahtani M, Abuzenadah A, Karim S, Schulten HJ, Al Sayyad AJ, Farsi HMA, Al-Maghrabi JA, Buhmaida A, Mirza Z, Alotibi R, Al-Ahmadi A, Alansari NA, Albogmi AA, Al-Quaiti MM, Ashgan FT, Bandah A, Al-Qahtani MH, Satar R, Rasool M, Ahmad W, Nazam N, Lone MI, Naseer MI, Jamal MS, Zaidi SK, Pushparaj PN, Jafri MA, Ansari SA, Alqahtani MH, Bashier H, Al Qahtani A, Mathew S, Nour AM, Alkhatabi H, Zenadah AMA, Buhmeida A, Assidi M, Al Qahtani M, Faheem M, Mathew S, Mathew S, Pushparaj PN, Al-Qahtani MH, Alhadrami HA, Dallol A, Abuzenadah A, Hussein IR, Chaudhary AG, Bader RS, Bassiouni R, Alquaiti M, Ashgan F, Schulten H, Alama MN, Al Qahtani MH, Lone MI, Nizam N, Ahmad W, Jafri MA, Rasool M, Ansari SA, Al-Qahtani MH, Alshihri E, Abu-Elmagd M, Alharbi L, Assidi M, Al-Qahtani M, Mathew S, Natesan PP, Al Qahtani M, Kalamegam G, Pushparaj PN, Khan F, Kadam R, Ahmed F, Assidi M, Sait KHW, Anfinan N, Al Qahtani M, Naseer MI, Chaudhary AG, Jamal MS, Mathew S, Mira LS, Pushparaj PN, Ansari SA, Rasool M, AlQahtani MH, Naseer MI, Chaudhary AG, Mathew S, Mira LS, Jamal MS, Sogaty S, Bassiouni RI, Rasool M, AlQahtani MH, Rasool M, Ansari SA, Jamal MS, Pushparaj PN, Sibiani AMS, Ahmad W, Buhmeida A, Jafri MA, Warsi MK, Naseer MI, Al-Qahtani MH, Rubi, Kumar K, Naqvi AAT, Ahmad F, Hassan MI, Jamal MS, Rasool M, AlQahtani MH, Ali A, Jarullah J, Rasool M, Buhmeida A, Khan S, Abdussami G, Mahfooz M, Kamal MA, Damanhouri GA, Jamal MS, Jarullah B, Jarullah J, Jarullah MSS, Ali A, Rasool M, Jamal MS, Assidi M, Abu-Elmagd M, Bajouh O, Pushparaj PN, Al-Qahtani M, Abuzenadah A, Jamal MS, Jarullah J, Mathkoor AEA, Alsalmi HMA, Oun AMM, Damanhauri GA, Rasool M, AlQahtani MH, Naseer MI, Rasool M, Sogaty S, Chudhary AG, Abutalib YA, Merico D, Walker S, Marshall CR, Zarrei M, Scherer SW, Al-Qahtani MH, Naseer MI, Faheem M, Chaudhary AG, Rasool M, Kalamegam G, Ashgan FT, Assidi M, Ahmed F, Zaidi SK, Jan MM, Al-Qahtani MH, Al-Zahrani M, Lary S, Hakamy S, Dallol A, Al-Ahwal M, Al-Maghrabi J, Dermitzakis E, Abuzenadah A, Buhmeida A, Al-Qahtani M, Al-refai AA, Saleh M, Yassien RI, Kamel M, Habeb RM, Filimban N, Dallol A, Ghannam N, Al-Qahtani M, Abuzenadah AM, Bibi F, Akhtar S, Azhar EI, Yasir M, Nasser MI, Jiman-Fatani AA, Sawan A, Lahzah RA, Ali A, Hassan SA, Hasnain SE, Tayubi IA, Abujabal HA, Magrabi AO, Khan F, Kalamegam G, Pushparaj PN, Abuzenada A, Kumosani TA, Barbour E, Al-Qahtani M, Shabaad M, Mathew S, Dallol A, Merdad A, Buhmeida A, Al-Qahtani M, Assidi M, Abu-Elmagd M, Gauthaman K, Gari M, Chaudhary A, Abuzenadah A, Pushparaj PN, Al-Qahtani M, Hassan SA, Tayubi IA, Aljahdali HMA, Al Nono R, Gari M, Alsehli H, Ahmed F, Abbas M, Kalamegam G, Al-Qahtani M, Mathew S, Khan F, Rasool M, Jamal MS, Naseer MI, Mirza Z, Karim S, Ansari S, Assidi M, Kalamegam G, Gari M, Chaudhary A, Abuzenadah A, Pushparaj PN, Al-Qahtani M, Abu-Elmagd M, Kalamegam G, Kadam R, Alghamdi MA, Shamy M, Costa M, Khoder MI, Assidi M, Pushparaj PN, Gari M, Al-Qahtani M, Kharrat N, Belmabrouk S, Abdelhedi R, Benmarzoug R, Assidi M, Al Qahtani MH, Rebai A, Dhamanhouri G, Pushparaj PN, Noorwali A, Alwasiyah MK, Bahamaid A, Alfakeeh S, Alyamani A, Alsehli H, Abbas M, Gari M, Mobasheri A, Kalamegam G, Al-Qahtani M, Faheem M, Mathew S, Pushparaj PN, Al-Qahtani MH, Mathew S, Faheem M, Mathew S, Pushparaj PN, Al-Qahtani MH, Jamal MS, Zaidi SK, Khan R, Bhatia K, Al-Qahtani MH, Ahmad S, AslamTayubi I, Tripathi M, Hassan SA, Shrivastava R, Tayubi IA, Hassan S, Abujabal HAS, Shah I, Jarullah B, Jamal MS, Jarullah J, Sheikh IA, Ahmad E, Jamal MS, Rehan M, Abu-Elmagd M, Tayubi IA, AlBasri SF, Bajouh OS, Turki RF, Abuzenadah AM, Damanhouri GA, Beg MA, Al-Qahtani M, Hammoudah SAF, AlHarbi KM, El-Attar LM, Darwish AMZ, Ibrahim SM, Dallol A, Choudhry H, Abuzenadah A, Awlia J, Chaudhary A, Ahmed F, Al-Qahtani M, Jafri MA, Abu-Elmagd M, Assidi M, Al-Qahtani M, khan I, Yasir M, Azhar EI, Al-basri S, Barbour E, Kumosani T, Khan F, Kalamegam G, Pushparaj PN, Abuzenada A, Kumosani TA, Barbour E, EL Sayed HM, Hafez EA, Schulten HJ, Elaimi AH, Hussein IR, Bassiouni RI, Alwasiyah MK, Wintle RF, Chaudhary A, Scherer SW, Al-Qahtani M, Mirza Z, Pillai VG, Karim S, Sharma S, Kaur P, Srinivasan A, Singh TP, Al-Qahtani M, Alotibi R, Al-Ahmadi A, Al-Adwani F, Hussein D, Karim S, Al-Sharif M, Jamal A, Al-Ghamdi F, Al-Maghrabi J, Baeesa SS, Bangash M, Chaudhary A, Schulten HJ, Al-Qahtani M, Faheem M, Pushparaj PN, Mathew S, Kumosani TA, Kalamegam G, Al-Qahtani M, Al-Allaf FA, Abduljaleel Z, Alashwal A, Taher MM, Bouazzaoui A, Abalkhail H, Ba-Hammam FA, Athar M, Kalamegam G, Pushparaj PN, Abu-Elmagd M, Ahmed F, Sait KH, Anfinan N, Gari M, Chaudhary A, Abuzenadah A, Assidi M, Al-Qahtani M, Mami NB, Haffani YZ, Medhioub M, Hamzaoui L, Cherif A, Azouz M, Kalamegam G, Khan F, Mathew S, Nasser MI, Rasool M, Ahmed F, Pushparaj PN, Al-Qahtani M, Turkistany SA, Al-harbi LM, Dallol A, Sabir J, Chaudhary A, Abuzenadah A, Al-Madoudi B, Al-Aslani B, Al-Harbi K, Al-Jahdali R, Qudaih H, Al Hamzy E, Assidi M, Al Qahtani M, Ilyas AM, Ahmed Y, Gari M, Ahmed F, Alqahtani M, Salem N, Karim S, Alhathli EM, Abusamra H, Eldin HFN, Al-Qahtani MH, Kumar S, Al-Adwani F, Hussein D, Al-Sharif M, Jamal A, Al-Ghamdi F, Al-Maghrabi J, Baeesa SS, Bangash M, Chaudhary A, Al-Qahtani M, Schulten HJ, Alamandi A, Alotibi R, Hussein D, Karim S, Al-Maghrabi J, Al-Ghamdi F, Jamal A, Baeesa SS, Bangash M, Chaudhary A, Schulten HJ, Al-Qahtani M, Subhi O, Bagatian N, Karim S, Al-Johari A, Al-Hamour OA, Al-Aradati H, Al-Mutawa A, Al-Mashat F, Al-Maghrabi J, Schulten HJ, Al-Qahtani M, Bagatian N, Subhi O, Karim S, Al-Johari A, Al-Hamour OA, Al-Mutawa A, Al-Aradati H, Al-Mashat F, Al-Qahtani M, Schulten HJ, Al-Maghrabi J, shah MW, Yasir M, Azhar EI, Al-Masoodi S, Haffani YZ, Azouz M, Khamla E, Jlassi C, Masmoudi AS, Cherif A, Belbahri L, Al-Khayyat S, Attas R, Abu-Sanad A, Abuzinadah M, Merdad A, Dallol A, Chaudhary A, Al-Qahtani M, Abuzenadah A, Bouazzi H, Trujillo C, Alwasiyah MK, Al-Qahtani M, Alotaibi M, Nassir R, Sheikh IA, Kamal MA, Jiffri EH, Ashraf GM, Beg MA, Aziz MA, Ali R, Rasool M, Jamal MS, Samman N, Abdussami G, Periyasamy S, Warsi MK, Aldress M, Al Otaibi M, Al Yousef Z, Boudjelal M, Buhmeida A, Al-Qahtani MH, AlAbdulkarim I, Ghazala R, Mathew S, Hamed MH, Assidi M, Al-Qahtani M, Qadri I, Sheikh IA, Abu-Elmagd M, Turki RF, Damanhouri GA, Beg MA, Suhail M, Qureshi A, Jamal A, Pushparaj PN, Al-Qahtani M, Qadri I, El-Readi MZ, Eid SY, Wink M, Isa AM, Alnuaim L, Almutawa J, Abu-Rafae B, Alasiri S, Binsaleh S. Abstracts from the 3rd International Genomic Medicine Conference (3rd IGMC 2015) : Jeddah, Kingdom of Saudi Arabia. 30 November - 3 December 2015

O1 Regulation of genes by telomere length over long distances

Jerry W. Shay

O2 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 epilepsy

Noriko Homma, Ruyun Zhou, Muhammad Imran Naseer, Adeel G. Chaudhary, Mohammed Al-Qahtani, Nobutaka Hirokawa

O3 Integration of metagenomics and metabolomics in gut microbiome research

Maryam Goudarzi, Albert J. Fornace Jr.

O4 A unique integrated system to discern pathogenesis of central nervous system tumors

Saleh 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 Damanhouri

O5 RPL27A is a target of miR-595 and deficiency contributes to ribosomal dysgenesis

Heba Alkhatabi

O6 Next generation DNA sequencing panels for haemostatic and platelet disorders and for Fanconi anaemia in routine diagnostic service

Anne Goodeve, Laura Crookes, Nikolas Niksic, Nicholas Beauchamp

O7 Targeted sequencing panels and their utilization in personalized medicine

Adel M. Abuzenadah

O8 International biobanking in the era of precision medicine

Jim Vaught

O9 Biobank and biodata for clinical and forensic applications

Bruce Budowle, Mourad Assidi, Abdelbaset Buhmeida

O10 Tissue microarray technique: a powerful adjunct tool for molecular profiling of solid tumors

Jaudah Al-Maghrabi

O11 The CEGMR biobanking unit: achievements, challenges and future plans

Abdelbaset Buhmeida, Mourad Assidi, Leena Merdad

O12 Phylomedicine of tumors

Sudhir Kumar, Sayaka Miura, Karen Gomez

O13 Clinical implementation of pharmacogenomics for colorectal cancer treatment

Angel Carracedo, Mahmood Rasool

O14 From association to causality: translation of GWAS findings for genomic medicine

Ahmed Rebai

O15 E-GRASP: an interactive database and web application for efficient analysis of disease-associated genetic information

Sajjad Karim, Hend F Nour Eldin, Heba Abusamra, Elham M Alhathli, Nada Salem, Mohammed H Al-Qahtani, Sudhir Kumar

O16 The supercomputer facility “AZIZ” at KAU: utility and future prospects

Hossam Faheem

O17 New research into the causes of male infertility

Ashok Agarwa

O18 The Klinefelter syndrome: recent progress in pathophysiology and management

Eberhard 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-Qahtani

O19 A new look to reproductive medicine in the era of genomics

Serdar Coskun

P1 Wnt signalling receptors expression in Saudi breast cancer patients

Muhammad 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 Abuzenadah

P2 Analysis of oxidative stress interactome during spermatogenesis: a systems biology approach to reproduction

Burak Ozkosem, Rick DuBois

P3 Interleukin-18 gene variants are strongly associated with idiopathic recurrent pregnancy loss.

Safia S Messaoudi, Maryam T Dandana, Touhami Mahjoub, Wassim Y Almawi

P4 Effect of environmental factors on gene-gene and gene-environment reactions: model and theoretical study applied to environmental interventions using genotype

S. Abdalla, M. Nabil Al-Aama

P5 Genomics and transcriptomic analysis of imatinib resistance in gastrointestinal stromal tumor

Asmaa 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 Kato

P6 In-Silico analysis of putative HCV epitopes against Pakistani human leukocyte antigen background: an approach towards development of future vaccines for Pakistani population

Sajid Mehmood, Naeem Mahmood Ashraf, Awais Asif, Muhammad Bilal, Malik Siddique Mehmood, Aadil Hussain

P7 Inhibition of AChE and BuChE with the natural compounds of Bacopa monerri for the treatment of Alzheimer’s disease: a bioinformatics approach

Qazi Mohammad Sajid Jamal, Mughees Uddin Siddiqui, Mohammad A. Alzohairy, Mohammad A. Al Karaawi

P8 Her2 expression in urothelial cell carcinoma of the bladder in Saudi Arabia

Taoufik Nedjadi, Jaudah Al-Maghrabi, Mourad Assidi, Heba Al-Khattabi, Adel Al-Ammari, Ahmed Al-Sayyad, Abdelbaset Buhmeida, Mohammed Al-Qahtani

P9 Association of angiotensinogen single nucleotide polymorphisms with Preeclampsia in patients from North Africa

Hédia Zitouni, Nozha Raguema, Marwa Ben Ali, Wided Malah, Raja Lfalah, Wassim Almawi, Touhami Mahjoub

P10 Systems biology analysis reveals relations between normal skin, benign nevi and malignant melanoma

Mohammed Elanbari, Andrey Ptitsyn

P11 The apoptotic effect of thymoquinone in Jurkat cells

Sana Mahjoub, Rabeb El Ghali, Bechir Achour, Nidhal Ben Amor, Mourad Assidi, Brahim N'siri, Hamid Morjani

P12 Sonic hedgehog contributes in bladder cancer invasion in Saudi Arabia

Taoufik Nedjadi, Adel Al-Ammari, Ahmed Al-Sayyad, Nada Salem, Esam Azhar, Jaudah Al-Maghrabi

P13 Association of Interleukin 18 gene promoter polymorphisms - 607A/C and -137 G/C with colorectal cancer onset in a sample of Tunisian population

Vera Chayeb, Maryam Dendena, Hedia Zitouni, Khedija Zouari-Limayem, Touhami Mahjoub

P14 Pathological expression of interleukin-6, -11, leukemia inhibitory factor and their receptors in tubal gestation with and without tubal cytomegalovirus infection

Bassem Refaat, Ahmed M Ashshi, Sarah A Batwa

P15 Phenotypic and genetic profiling of avian pathogenic and human diarrhegenic Escherichia coli in Egypt

Hazem Ramadan, Amal Awad, Ahmed Ateya

P16 Cancer-targeting dual gene virotherapy as a promising therapeutic strategy for treatment of hepatocellular carcinoma

Adel Galal Ahmed El-Shemi, Ahmad Ashshi, Mohammed Basalamah, Youjin Na, Chae-Ok YUN

P17 Cancer dual gene therapy with oncolytic adenoviruses expressing TRAIL and IL-12 transgenes markedly eradicated human hepatocellular carcinoma both in vitro and in vivo

Adel Galal Ahmed El-Shemi, Ahmad Ashshi, Mohammed Basalamah, Youjin Na, Chae-Ok Yun

P18 Therapy with paricalcitol attenuates tumor growth and augments tumoricidal and anti-oncogenic effects of 5-fluorouracil on animal model of colon cancer

Adel Galal El-Shemi, Bassem Refaat, Osama Kensara, Amr Abdelfattah

P19 The effects of Rubus idaeus extract on normal human lymphocytes and cancer cell line

Batol Imran Dheeb, Mohammed M. F. Al-Halbosiy, Rghad Kadhim Al lihabi, Basim Mohammed Khashman

P20 Etanercept, a TNF-alpha inhibitor, alleviates mechanical hypersensitivity and spontaneous pain in a rat model of chemotherapy-induced neuropathic pain

Djouhri, Laiche, Chaudhary Adeel, Nedjadi, Taoufik

P21 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 Jackson

P22 Involvement of interleukin-1 in vitiligo pathogenesis

Mala Singh, Mohmmad Shoab Mansuri, Shahnawaz D. Jadeja, Hima Patel, Yogesh S. Marfatia, Rasheedunnisa Begum

P23 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-Ruby

P24 Analysis of binding properties of angiotensin-converting enzyme 2 through in silico method

S. M. A. Shahid, Qazi Mohammad Sajid Jamal, J. M. Arif, Mohtashim Lohani

P25 Relationship of genetics markers cis and trans to the β-S globin gene with fetal hemoglobin expression in Tunisian sickle cell patients

Moumni Imen, Chaouch Leila, Ouragini Houyem, Douzi Kais, Chaouachi Dorra Mellouli Fethi, Bejaoui Mohamed, Abbes Salem

P26 Analysis of estrogen receptor alpha gene polymorphisms in breast cancer: link to genetic predisposition in Sudanese women

Areeg Faggad, Amanuel T Gebreslasie, Hani Y Zaki, Badreldin E Abdalla

P27 KCNQI gene polymorphism and its association with CVD and T2DM in the Saudi population

Maha 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 Acharya

P28 Clinical, neuroimaging and cytogenetic study of a patient with microcephaly capillary malformation syndrome

Maha S. Zaki, Hala T. El-Bassyouni, Marwa I. Shehab

P29 Altered expression of CD200R1 on dendritic cells of patients with inflammatory bowel diseases: in silico investigations and clinical evaluations

Mohammed F. Elshal, Kaleemuddin M., Alia M. Aldahlawi, Omar Saadah,

J. Philip McCoy

P30 Development of real time PCR diagnostic protocol specific for the Saudi Arabian H1N1 viral strains

Adel E El-Tarras, Nabil S Awad, Abdulla A Alharthi, Mohamed M M Ibrahim

P31 Identification of novel genetic variations affecting Osteoarthritis patients

Haneen S Alsehli, Ashraf Dallol, Abdullah M Gari, Mohammed M Abbas, Roaa A Kadam, Mazen M. Gari, Mohmmed H Alkaff, Adel M Abuzenadah, Mamdooh A Gari

P32 An integrated database of GWAS SNVs and their evolutionary properties

Heba Abusamra, Sajjad Karim, Hend F Nour eldin, Elham M Alhathli, Nada Salem, Sudhir Kumar, Mohammed H Al-Qahtani

P33 Familial hypercholesterolemia in Saudi Arabia: prime time for a national registry and genetic analysis

Fatima A. Moradi, Omran M. Rashidi, Zuhier A. Awan

P34 Comparative genomics and network-based analyses of early hepatocellular carcinoma

Ibrahim Hamza Kaya, Olfat Al-Harazi, Dilek Colak

P35 A TALEN-based oncolytic viral vector approach to knock out ABCB1 gene mediated chemoresistance in cancer stem cells

Nabila A Alkousi, Takis Athanasopoulos

P36 Cartilage differentiation and gene expression of synovial fluid mesenchymal stem cells derived from osteoarthritis patients

Afnan O Bahmaid, Etimad A Alhwait, Mamdooh A Gari, Haneen S Alsehli, Mohammed M Abbas, Mohammed H Alkaf, Roaa Kadam, Ashraf Dallol, Gauthaman Kalamegam

P37 E-GRASP: Adding an evolutionary component to the genome-wide repository of associations (GRASP) resource

Hend F Nour Eldin, Sajjad Karim, Heba Abusamra, Elham Alhathli, Nada Salem, Mohammed H Al-Qahtani, Sudhir Kumar

P38 Screening of AGL gene mutation in Saudi family with glycogen storage disease Type III

Salma N Alsayed, Fawziah H Aljohani, Samaher M Habeeb, Rawan A Almashali, Sulman Basit, Samia M Ahmed

P39 High throughput proteomic data suggest modulation of cAMP dependent protein kinase A and mitochondrial function in infertile patients with varicocele

Rakesh Sharma, Ashok Agarwal, Damayanthi Durairajanayagam, Luna Samanta, Muhammad Abu-Elmagd, Adel M. Abuzenadah, Edmund S. Sabanegh, Mourad Assidi, Mohammed Al-Qahtani

P40 Significant protein profile alterations in men with primary and secondary infertility

Ashok Agarwal, Rakesh Sharma, Luna Samanta, Damayanthi Durairajanayagam, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-Qahtani, Adel M. Abuzenadah, Edmund S. Sabanegh

P41 Spermatozoa maturation in infertile patients involves compromised expression of heat shock proteins

Luna Samanta, Ashok Agarwal, Rakesh Sharma, Zhihong Cui, Mourad Assidi, Adel M. Abuzenadah, Muhammad Abu-Elmagd, Mohammed Al-Qahtani

P42 Array comparative genomic hybridization approach to search genomic answers for spontaneous recurrent abortion in Saudi Arabia

Alaa 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-Qahtani

P43 Global gene expression profiling of Saudi kidney cancer patients

Sajjad 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-Qahtani

P44 Downregulated StAR gene and male reproductive dysfunction caused by nifedipine and ethosuximide

Rasha A Ebiya, Samia M Darwish, Metwally M. Montaser

P45 Clustering based gene expression feature selection method: A computational approach to enrich the classifier efficiency of differentially expressed genes

Heba Abusamra, Vladimir B. Bajic

P46 Prognostic significance of Osteopontin expression profile in colorectal carcinoma

Jaudah Al-Maghrabi, Wafaey Gomaa, Mehenaz Hanbazazh, Mahmoud Al-Ahwal, Asia Al-Harbi, Wejdan Al-Qahtani, Saher Hakamy, Ghali Baba, Abdelbaset Buhmeida, Mohammed Al-Qahtani

P47 High Glypican-3 expression pattern predicts longer disease-specific survival in colorectal carcinoma

Jaudah Al-Maghrabi, Abdullah Al-Harbi, Mahmoud Al-Ahwal, Asia Al-Harbi, Wejdan Al-Qahtani, Sahar Hakamy, Ghalia Baba, Abdelbaset Buhmeida, Mohammed Al-Qahtani

P48 An evolutionary re-assessment of GWAS single nucleotide variants implicated in the Cholesterol traits

Elham M Alhathli, Sajjad Karim, Nada Salem, Hend Nour Eldin, Heba Abusamra, Sudhir Kumar, Mohammed H Al-Qahtani

P49 Derivation and characterization of human Wharton’s jelly stem cells (hWJSCs) in vitro for future therapeutic applications

Aisha A Alyamani, Gauthaman Kalamegam, Etimad A Alhwait, Mamdooh A Gari, Mohammed M Abbas, Mohammed H Alkaf, Haneen S Alsehli, Roaa A Kadam, Mohammed Al-Qahtani

P50 Attitudes of healthcare students toward biomedical research in the post-genomic era

Rawan Gadi, Abdelbaset Buhmeida, Mourad Assidi , Adeel Chaudhary, Leena Merdad

P51 Evaluation of the immunomodulatory effects of thymoquinone on human bone marrow mesenchymal stem cells (BM-MSCs) from osteoarthritic patients

Saadiah M Alfakeeh, Etimad A Alhwait, Mamdooh A Gari, Mohammed M Abbas, Mohammed H Alkaf, Haneen S Alsehli, Roaa Kadam, Gauthaman Kalamegam

P52 Implication of IL-10 and IL-28 polymorphism with successful anti-HCV therapy and viral clearance

Rubi Ghazala, Shilu Mathew, M.Haroon Hamed, Mourad Assidi, Mohammed Al-Qahtani, Ishtiaq Qadri

P53 Selection of flavonoids against obesity protein (FTO) using in silico and in vitro approaches

Shilu Mathew, Lobna Mira, Manal Shaabad, Shireen Hussain, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-Qahtani

P54 Computational selection and in vitro validation of flavonoids as new antidepressant agents

Shilu Mathew, Manal Shaabad, Lobna Mira, Shireen Hussain, Mourad Assidi, Muhammad Abu-Elmagd, Mohammed Al-Qahtani

P55 In Silico prediction and prioritization of aging candidate genes associated with

progressive telomere shortening

Ahmed Rebai, Mourad Assidi, Abdelbaset Buhmeida, Muhammad Abu-Elmagd, Ashraf Dallol, Jerry W Shay

P56 Identification of new cancer testis antigen genes in diverse types of malignant human tumour cells

Mikhlid H Almutairi

P57 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 Budowle

P58 Flow cytometry approach towards treatment men infertility in Saudi Arabia

Muhammad Abu-Elmagd, Farid Ahmed, Ashraf Dallol, Mourad Assidi, Taha Abo Almagd, Sahar Hakamy, Ashok Agarwal, Muhammad Al-Qahtani, Adel Abuzenadah

P59 Tissue microarray based validation of CyclinD1 expression in renal cell carcinoma of Saudi kidney patients

Sajjad 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-Qahtani

P60 Assessment of gold nanoparticles in molecular diagnostics and DNA damage studies

Rukhsana 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 Alqahtani

P61 Surfing the biospecimen management and processing workflow at CEGMR Biobank

Hanan Bashier, Abrar Al Qahtani, Shilu Mathew, Amal M. Nour, Heba Alkhatabi, Adel M. Abu Zenadah, Abdelbaset Buhmeida, Mourad Assidi, Muhammed Al Qahtani

P62 Autism Spectrum Disorder: knowledge, attitude and awareness in Jeddah, Kingdom of Saudi Arabia

Muhammad Faheem, Shilu Mathew, Shiny Mathew, Peter Natesan Pushparaj, Mohammad H. Al-Qahtani

P63 Simultaneous genetic screening of the coagulation pathway genes using the Thromboscan targeted sequencing panel

Hani A. Alhadrami, Ashraf Dallol, Adel Abuzenadah

P64 Genome wide array comparative genomic hybridization analysis in patients with syndromic congenital heart defects

Ibtessam R. Hussein, Adeel G. Chaudhary, Rima S Bader, Randa Bassiouni, Maha Alquaiti, Fai Ashgan, Hans Schulten, Mohamed Nabil Alama, Mohammad H. Al Qahtani

P65 Toxocogenetic evaluation of 1, 2-Dichloroethane in bone marrow, blood and cells of immune system using conventional, molecular and flowcytometric approaches

Mohammad I Lone, Nazia Nizam, Waseem Ahmad, Mohammad A Jafri, Mahmood Rasool, Shakeel A Ansari, Muhammed H Al-Qahtani

P66 Molecular cytogenetic diagnosis of sexual development disorders in newborn: A case of ambiguous genitalia

Eradah Alshihri, Muhammad Abu-Elmagd, Lina Alharbi, Mourad Assidi, Mohammed Al-Qahtani

P67 Identification of disease specific gene expression clusters and pathways in hepatocellular carcinoma using In Silico methodologies

Shilu Mathew, Peter Pushparaj Natesan, Muhammed Al Qahtani

P68 Human Wharton’s Jelly stem cell conditioned medium inhibits primary ovarian cancer cells in vitro: Identification of probable targets and mechanisms using systems biology

Gauthaman Kalamegam, Peter Natesan Pushparaj, Fazal Khan, Roaa Kadam, Farid Ahmed, Mourad Assidi, Khalid Hussain Wali Sait, Nisreen Anfinan, Mohammed Al Qahtani

P69 Mutation spectrum of ASPM (Abnormal Spindle-like, Microcephaly-associated) gene in Saudi Arabian population

Muhammad I Naseer, Adeel G Chaudhary, Mohammad S Jamal, Shilu Mathew, Lobna S Mira, Peter N Pushparaj, Shakeel A Ansari, Mahmood Rasool, Mohammed H AlQahtani

P70 Identification and characterization of novel genes and mutations of primary microcephaly in Saudi Arabian population

Muhammad I Naseer, Adeel G Chaudhary, Shilu Mathew, Lobna S Mira, Mohammad S Jamal, Sameera Sogaty, Randa I Bassiouni, Mahmood Rasool, Mohammed H AlQahtani

P71 Molecular genetic analysis of hereditary nonpolyposis colorectal cancer (Lynch Syndrome) in Saudi Arabian population

Mahmood 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-Qahtani

P72 Function predication of hypothetical proteins from genome database of chlamydia trachomatis

Rubi, Kundan Kumar, Ahmad AT Naqvi, Faizan Ahmad, Md I Hassan, Mohammad S Jamal, Mahmood Rasool, Mohammed H AlQahtani

P73 Transcription factors as novel molecular targets for skin cancer

Ashraf Ali, Jummanah Jarullah, Mahmood Rasool, Abdelbasit Buhmeida, Shahida Khan, Ghufrana Abdussami, Maryam Mahfooz, Mohammad A Kamal, Ghazi A Damanhouri, Mohammad S Jamal

P74 An In Silico analysis of Plumbagin binding to apoptosis executioner: Caspase-3 and Caspase-7

Bushra Jarullah, Jummanah Jarullah, Mohammad SS Jarullah, Ashraf Ali, Mahmood Rasool, Mohammad S Jamal

P75 Single cell genomics applications for preimplantation genetic screening optimization: Comparative analysis of whole genome amplification technologies

Mourad Assidi, Muhammad Abu-Elmagd, Osama Bajouh, Peter Natesan Pushparaj, Mohammed Al-Qahtani, Adel Abuzenadah

P76 ZFP36 regulates miRs-34a in anti-IgM triggered immature B cells

Mohammad S Jamal, Jummanah Jarullah, Abdulah EA Mathkoor, Hashim MA Alsalmi, Anas MM Oun, Ghazi A Damanhauri, Mahmood Rasool, Mohammed H AlQahtani

P77 Identification of a novel mutation in the STAMBP gene in a family with microcephaly-capillary malformation syndrome

Muhammad 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-Qahtani

P78 Copy number variations in Saudi patients with intellectual disability and epilepsy

Muhammad 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-Qahtani

P79 Prognostic significance of CD44 expression profile in colorectal carcinoma

Maryam Al-Zahrani, Sahira Lary, Sahar Hakamy, Ashraf Dallol, Mahmoud Al-Ahwal, Jaudah Al-Maghrabi, Emmanuel Dermitzakis, Adel Abuzenadah, Abdelbaset Buhmeida, Mohammed Al-Qahtani

P80 Association of the endothelial nitric oxide synthase (eNOS) gene G894T polymorphism with hypertension risk and complications

Abeer A Al-refai, Mona Saleh, Rehab I Yassien, Mahmmoud Kamel, Rabab M Habeb

P81 SNPs array to screen genetic variation among diabetic patients

Najlaa Filimban, Ashraf Dallol, Nadia Ghannam, Mohammed Al-Qahtani, Adel Mohammed Abuzenadah

P82 Detection and genotyping of Helicobacter pylori among gastric cancer patients from Saudi Arabian population

Fehmida Bibi, Sana Akhtar, Esam I. Azhar, Muhammad Yasir, Muhammad I. Nasser, Asif A. Jiman-Fatani, Ali Sawan

P83 Antimicrobial drug resistance and molecular detection of susceptibility to Fluoroquinolones among clinical isolates of Salmonella species from Jeddah-Saudi Arabia

Ruaa A Lahzah, Asho Ali

P84 Identification of the toxic and virulence nature of MAP1138c protein of Mycobacterium avium subsp. paratuberculosis

Syed A Hassan, Seyed E Hasnain, Iftikhar A Tayubi, Hamza A Abujabal, Alaa O Magrabi

P85 In vitro and in silico evaluation of miR137 in human breast cancer

Fazal Khan, Gauthaman Kalamegam, Peter Natesan Pushparaj, Adel Abuzenada, Taha Abduallah Kumosani, Elie Barbour, Mohammed Al-Qahtani

P86 Auruka gene is over-expressed in Saudi breast cancer

Manal Shabaad, Shilu Mathew, Ashraf Dallol, Adnan Merdad, Abdelbaset Buhmeida, Mohammed Al-Qahtani

P87 The potential of immunogenomics in personalized healthcare

Mourad Assidi, Muhammad Abu-Elmagd, Kalamegam Gauthaman, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Peter Natesan Pushparaj, Mohammed Al-Qahtani

P88 In Silico physiochemical and structural characterization of a putative ORF MAP0591 and its implication in the pathogenesis of Mycobacterium paratuberculosis in ruminants and humans

Syed A Hassan, Iftikhar A Tayubi, Hani MA Aljahdali

P89 Effects of heat shock on human bone marrow mesenchymal stem cells (BM-MSCs): Implications in regenerative medicine

Reham Al Nono, Mamdooh Gari, Haneen Alsehli, Farid Ahmed, Mohammed Abbas, Gauthaman Kalamegam, Mohammed Al-Qahtani

P90 In Silico analyses of the molecular targets of Resveratrol unravels its importance in mast cell mediated allergic responses

Shilu 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-Qahtani

P91 Effects of environmental particulate matter on bone-marrow mesenchymal stem cells

Muhammad 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-Qahtani

P92 Distinctive charge clusters in human virus proteomes

Najla Kharrat, Sabrine Belmabrouk, Rania Abdelhedi, Riadh Benmarzoug, Mourad Assidi, Mohammed H. Al Qahtani, Ahmed Rebai

P93 In vitro experimental model and approach in identification of new biomarkers of inflammatory forms of arthritis

Ghazi 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-Qahtani

P94 Molecular docking of GABA_A receptor subunit γ-2 with novel anti-epileptic compounds

Muhammad Faheem, Shilu Mathew, Peter Natesan Pushparaj, Mohammad H. Al-Qahtani

P95 Breast cancer knowledge, awareness, and practices among Saudi females residing in Jeddah

Shilu Mathew, Muhammad Faheem, Shiny Mathew, Peter Natesan Pushparaj, Mohammad H. Al-Qahtani

P96 Anti-inflammatory role of Sesamin by Attenuation of Iba1/TNF-α/ICAM-1/iNOS signaling in Diabetic Retinopathy

Mohammad Sarwar Jamal, Syed Kashif Zaidi, Raziuddin Khan, Kanchan Bhatia, Mohammed H. Al-Qahtani, Saif Ahmad

P97 Identification of drug lead molecule against vp35 protein of Ebola virus: An In-Silico approach

Iftikhar AslamTayubi, Manish Tripathi, Syed Asif Hassan, Rahul Shrivastava

P98 An approach to personalized medicine from SNP-calling through disease analysis using whole exome-sequencing of three sub-continental populations

Iftikhar A Tayubi, Syed Hassan, Hamza A.S Abujabal

P99 Low versus high frequency of Glucose –6 – Phosphate Dehydrogenase (G6PD) deficiency in urban against tribal population of Gujarat – A signal to natural selection

Ishani Shah, Bushra Jarullah, Mohammad S Jamal, Jummanah Jarullah

P100 Spontaneous preterm birth and single nucleotide gene polymorphisms: a recent update

Ishfaq 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-Qahtani

P101 Prevalence of congenital heart diseases among Down syndrome cases in Saudi Arabia: role of molecular genetics in the pathogenesis

Sahar AF Hammoudah, Khalid M AlHarbi, Lama M El-Attar, Ahmed MZ Darwish

P102 Combinatorial efficacy of specific pathway inhibitors in breast cancer cells

Sara M Ibrahim, Ashraf Dallol_, Hani Choudhry, Adel Abuzenadah, Jalaludden Awlia, Adeel Chaudhary, Farid Ahmed, Mohammed Al-Qahtani

P103 MiR-143 and miR-145 cluster as potential replacement medicine for the treatment of cancer

Mohammad A Jafri, Muhammad Abu-Elmagd, Mourad Assidi, Mohammed Al-Qahtani

P104 Metagenomic profile of gut microbiota during pregnancy in Saudi population

Imran khan, Muhammad Yasir, Esam I. Azhar, Sameera Al-basri, Elie Barbour, Taha Kumosani

P105 Exploration of anticancer targets of selected metabolites of Phoenix dactylifera L. using systems biological approaches

Fazal Khan, Gauthaman Kalamegam, Peter Natesan Pushparaj, Adel Abuzenada, Taha Abduallah Kumosani, Elie Barbour

P106 CD226 and CD40 gene polymorphism in susceptibility to Juvenile rheumatoid arthritis in Egyptian patients

Heba M. EL Sayed, Eman A. Hafez

P107 Paediatric exome sequencing in autism spectrum disorder ascertained in Saudi families

Hans-Juergen Schulten, Aisha Hassan Elaimi, Ibtessam R Hussein, Randa Ibrahim Bassiouni, Mohammad Khalid Alwasiyah, Richard F Wintle, Adeel Chaudhary, Stephen W Scherer, Mohammed Al-Qahtani

P108 Crystal structure of the complex formed between Phospholipase A₂ and the central core hydrophobic fragment of Alzheimer’s β- amyloid peptide: a reductionist approach

Zeenat Mirza, Vikram Gopalakrishna Pillai, Sajjad Karim, Sujata Sharma, Punit Kaur, Alagiri Srinivasan, Tej P Singh, Mohammed Al-Qahtani

P109 Differential expression profiling between meningiomas from female and male patients

Reem 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-Qahtani

P110 Neurospheres as models of early brain development and therapeutics

Muhammad Faheem, Peter Natesan Pushparaj, Shilu Mathew, Taha Abdullah Kumosani, Gauthaman Kalamegam, Mohammed Al-Qahtani

P111 Identification of a recurrent causative missense mutation p.(W577C) at the LDLR exon 12 in familial hypercholesterolemia affected Saudi families

Faisal A Al-Allaf, Zainularifeen Abduljaleel, Abdullah Alashwal, Mohiuddin M. Taher, Abdellatif Bouazzaoui, Halah Abalkhail, Faisal A. Ba-Hammam, Mohammad Athar

P112 Epithelial ovarian carcinoma (EOC): Systems oncological approach to identify diagnostic, prognostic and therapeutic biomarkers

Gauthaman Kalamegam, Peter Natesan Pushparaj, Muhammad Abu-Elmagd, Farid Ahmed Khalid HussainWali Sait, Nisreen Anfinan, Mamdooh Gari, Adeel Chaudhary, Adel Abuzenadah, Mourad Assidi, Mohammed Al-Qahtani

P113 Crohn’s disease phenotype in northern Tunisian population

Naira Ben Mami, Yosr Z Haffani, Mouna Medhioub, Lamine Hamzaoui, Ameur Cherif, Msadok Azouz

P114 Establishment of In Silico approaches to decipher the potential toxicity and mechanism of action of drug candidates and environmental agents

Gauthaman Kalamegam, Fazal Khan, Shilu Mathew, Mohammed Imran Nasser, Mahmood Rasool, Farid Ahmed, Peter Natesan Pushparaj, Mohammed Al-Qahtani

P115 1q Gain predicts poor prognosis marker for young breast cancer patients

Shereen A Turkistany, Lina M Al-harbi, Ashraf Dallol, Jamal Sabir, Adeel Chaudhary, Adel Abuzenadah

P116 Disorders of sex chromosomes in a diagnostic genomic medicine unit in Saudi Arabia: Prevalence, diagnosis and future guidelines

Basmah Al-Madoudi, Bayan Al-Aslani, Khulud Al-Harbi, Rwan Al-Jahdali, Hanadi Qudaih, Emad Al Hamzy, Mourad Assidi, Mohammed Al Qahtani

P117 Combination of WYE354 and Sunitinib demonstrate synergistic inhibition of acute myeloid leukemia in vitro

Asad M Ilyas, Youssri Ahmed, Mamdooh Gari, Farid Ahmed, Mohammed Alqahtani

P118 Integrated use of evolutionary information in GWAS reveals important SNPs in Asthma

Nada Salem, Sajjad Karim, Elham M Alhathli, Heba Abusamra, Hend F Nour Eldin, Mohammed H Al-Qahtani, Sudhir Kumar

P119 Assessment of BRAF, IDH1, IDH2, and EGFR mutations in a series of primary brain tumors

Fatima 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 Schulten

P120 Expression profiles distinguish oligodendrogliomas from glioblastoma multiformes with or without oligodendroglioma component

Alaa 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-Qahtani

P121 Hierarchical clustering in thyroid goiters and hyperplastic lesions

Ohoud 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-Qahtani

P122 Differential expression analysis in thyroiditis and papillary thyroid carcinomas with or without coexisting thyroiditis

Nadia 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-Maghrabi

P123 Metagenomic analysis of waste water microbiome in Sausdi Arabia

Muhammad W shah, Muhammad Yasir, Esam I Azhar, Saad Al-Masoodi

P124 Molecular characterization of Helicobacter pylori from faecal samples of Tunisian patients with gastric cancer

Yosr Z Haffani, Msadok Azouz, Emna Khamla, Chaima Jlassi, Ahmed S. Masmoudi, Ameur Cherif, Lassaad Belbahri

P125 Diagnostic application of the oncoscan^© panel for the identification of hereditary cancer syndrome

Shadi Al-Khayyat, Roba Attas, Atlal Abu-Sanad, Mohammed Abuzinadah, Adnan MerdadAshraf Dallol, Adeel Chaudhary, Mohammed Al-Qahtani, Adel Abuzenadah

P126 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-Qahtani

P127 Case report: a rare homozygous deletion mutation of TMEM70 gene associated with 3-Methylglutaconic Aciduria and cataract in a Saudi patient

Maha Alotaibi, Rami Nassir

P128 Isolation and purification of antimicrobial milk proteins

Ishfaq A Sheikh, Mohammad A Kamal, Essam H Jiffri, Ghulam M Ashraf, Mohd A Beg

P129 Integrated analysis reveals association of ATP8B1 gene with colorectal cancer

Mohammad 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 AlAbdulkarim

P130 Implication of IL-10 and IL-28 polymorphism with successful anti-HCV therapy and viral clearance

Rubi Ghazala, Shilu Mathew, M. Haroon Hamed, Mourad Assidi, Mohammed Al-Qahtani, Ishtiaq Qadri

P131 Interactions of endocrine disruptor di-(2-ethylhexyl) phthalate (DEHP) and its metabolite mono-2-ethylhexyl phthalate (MEHP) with progesterone receptor

Ishfaq A Sheikh, Muhammad Abu-Elmagd, Rola F Turki, Ghazi A Damanhouri, Mohd A. Beg

P132 Association of HCV nucleotide polymorphism in the development of hepatocellular carcinoma

Mohd Suhail, Abid Qureshi, Adil Jamal, Peter Natesan Pushparaj, Mohammad Al-Qahtani, Ishtiaq Qadri

P133 Gene expression profiling by DNA microarrays in colon cancer treated with chelidonine alkaloid

Mahmoud Z El-Readi, Safaa Y Eid, Michael Wink

P134 Successful in vitro fertilization after eight failed trials

Ahmed M. Isa, Lulu Alnuaim, Johara Almutawa, Basim Abu-Rafae, Saleh Alasiri, Saleh Binsaleh

P135 Genetic sensitivity analysis using SCGE, cell cycle and mitochondrial membrane potential in OPs stressed leukocytes in Rattus norvegicus through flow cytometric input

Nazia Nazam, Mohamad I Lone, Waseem Ahmad, Shakeel A Ansari, Mohamed H Alqahtani

Effects of the Ion PGM™ Hi-Q™ sequencing chemistry on sequence data quality

Massively parallel sequencing (MPS) offers substantial improvements over current forensic DNA typing methodologies such as increased resolution, scalability, and throughput. The Ion PGM™ is a promising MPS platform for analysis of forensic biological evidence. The system employs a sequencing-by-synthesis chemistry on a semiconductor chip that measures a pH change due to the release of hydrogen ions as nucleotides are incorporated into the growing DNA strands. However, implementation of MPS into forensic laboratories requires a robust chemistry. Ion Torrent's Hi-Q™ Sequencing Chemistry was evaluated to determine if it could improve on the quality of the generated sequence data in association with selected genetic marker targets. The whole mitochondrial genome and the HID-Ion STR 10-plex panel were sequenced on the Ion PGM™ system with the Ion PGM™ Sequencing 400 Kit and the Ion PGM™ Hi-Q™ Sequencing Kit. Concordance, coverage, strand balance, noise, and deletion ratios were assessed in evaluating the performance of the Ion PGM™ Hi-Q™ Sequencing Kit. The results indicate that reliable, accurate data are generated and that sequencing through homopolymeric regions can be improved with the use of Ion Torrent's Hi-Q™ Sequencing Chemistry. Overall, the quality of the generated sequencing data supports the potential for use of the Ion PGM™ in forensic genetic laboratories.

D5S2500 is an ambiguously characterized STR: Identification and description of forensic microsatellites in the genomics age

In the process of establishing short tandem repeat (STR) sequence variant nomenclature guidelines in anticipation of expanded forensic multiplexes for massively parallel sequencing (MPS), it was discovered that the STR D5S2500 has multiple positions and genomic characteristics reported. This ambiguity is because the marker named D5S2500 consists of two different microsatellites forming separate components in the capillary electrophoresis multiplexes of Qiagen's HDplex (Hilden, Germany) and AGCU ScienTech's non-CODIS STR 21plex (Wuxi, Jiangsu, China). This study outlines the genomic details used to identify each microsatellite and reveals the D5S2500 marker in HDplex has the correctly assigned STR name, while the D5S2500 marker in the AGCU 21plex, closely positioned a further 1643 nucleotides in the human reference sequence, is an unnamed microsatellite. The fact that the D5S2500 marker has existed as two distinct STR loci undetected for almost ten years, even with reported discordant genotypes for the standard control DNA, underlines the need for careful scrutiny of the genomic properties of forensic STRs, as they become adapted for sequence analysis with MPS systems. We make the recommendation that precise chromosome location data must be reported for any forensic marker under development but not in common use, so that the genomic characteristics of the locus are validated to the same level of accuracy as its allelic variation and forensic performance. To clearly differentiate each microsatellite, we propose the name D5S2800 be used to identify the Chromosome-5 STR in the AGCU 21plex.

Blind study evaluation illustrates utility of the Ion PGM™ system for use in human identity DNA typing

Aim

To perform a blind study to assess the capability of the Ion Personal Genome Machine™ (PGM) system to sequence forensically relevant genetic marker panels and to characterize unknown individuals for ancestry and possible relatedness.

Methods

Twelve genomic samples were provided by a third party for blinded genetic analysis. For these 12 samples, the mitochondrial genome and three PGM™ panels containing human identity single nucleotide polymorphisms (SNPs), ancestry informative SNPs, and short tandem repeats (STRs) were sequenced on the PGM™ system and analyzed.

Results

All four genetic systems were run and analyzed on the PGM™ system in a reasonably quick time frame. Completeness of genetic profiles, depth of coverage, strand balance, and allele balance were informative metrics that illustrated the quality and reliability of the data produced. SNP genotypes allowed for identification of sex, paternal lineage, and population ancestry. STR genotypes were shown to be in complete concordance with genotypes generated by standard capillary electrophoresis-based technologies. Variants in the mitochondrial genome data provided information on population background and maternal relationships.

Conclusion

All results from analysis of the 12 genomic samples were consistent with sample information provided by the sample providers at the end of the blinded study. The relatively easy identification of intra-STR allele SNPs offered the potential for increased discrimination power. The promising nature of these results warrants full validation studies of this massively parallel sequencing technology and its further development for forensic data analysis.

Modified DOP-PCR for improved STR typing of degraded DNA from human skeletal remains and bloodstains

Forensic and ancient DNA samples often are damaged and in limited quantity as a result of exposure to harsh environments and the passage of time. Several strategies have been proposed to address the challenges posed by degraded and low copy templates, including a PCR based whole genome amplification method called degenerate oligonucleotide-primed PCR (DOP-PCR). This study assessed the efficacy of four modified versions of the original DOP-PCR primer that retain at least a portion of the 5' defined sequence and alter the number of bases on the 3' end. The use of each of the four modified primers resulted in improved STR profiles from environmentally-damaged bloodstains, contemporary human skeletal remains, American Civil War era bone samples, and skeletal remains of WWII soldiers over those obtained by previously described DOP-PCR methods and routine STR typing. Additionally, the modified DOP-PCR procedure allows for a larger volume of DNA extract to be used, reducing the need to concentrate the sample and thus mitigating the effects of concurrent concentration of inhibitors.