DNA Bank Research Articles

Friedreich Ataxia: Treatment with Genetic Approach

Friedreich ataxia (FA) is a disorder in the nervous system inherited according to the Mendel’s first law. Mutations in the FXN gene trigger the FA disorder. The FXN gene occupies chromosome 9q21.11 in the chromosome map. Mutations in the FXN gene consist of four classes of alleles. These include normal alleles, changeable normal alleles, complete penetrance alleles, and borderline alleles. Currently, there is no efficient treatment for this disorder. To slow down FA, genetic approach can be used. The approach may comprise genetic counseling and use of gene therapy. In genetic counseling, if both parents are carriers, a child has a 25 % FA. To detect people with carrier, amniocentesis can be used for instance. Preimplantation FA diagnostic can also be made. In gene therapy, DNA banking is needed. It is useful to study Friedreich ataxia for treatment of this disorder. Gene therapy is a method to correct damaged cells of patients. In this article, the author shows viral vectors such as HSV-1 amplicon vectors and lentivirus vectors as gene shipping vehicles. Both can restore the normal point of frataxin. These results show that gene therapy is a promising tool to treat FA disorder.

Addressing Hereditary Cancer Risk at the End of Life.

Oncology guidelines clearly outline evidence-based recommendations for patients with newly diagnosed cancer to help oncologists determine which patients are appropriate for a genetic assessment. Ideally, patients with newly diagnosed cancer, who have personal or family histories suggestive of hereditary cancer predisposition, are referred for genetics work up in the nonurgent setting. However, in some cases, a genetics work up is delayed until the end of life. This is a time of heightened stress and additional obstacles, including discordance between family members regarding the obtainment of genetic information, paying for testing, selecting a surrogate to receive and disperse information in the case of a patient's death, and the use of DNA banking for future evaluation. To meaningfully participate and support patients, family members, and our colleagues facing requests at the end of life for genetic testing, we provide a practical approach and highlight resources to effectively engage in this rising challenge.

Germline mutations of PALB2 gene in a sequential series of Chinese patients with breast cancer.

1530 Background: PALB2 (Partner and Localizer of BRCA2) is recently recognized as a breast cancer predisposition gene, which plays a critical role in genome maintenance via interacting with BRCA1/2 and RAD51 when DNA break. Germline loss-of-function mutations in PALB2 lead to increased breast cancer risk. Since the germline mutation frequency of PALB2 is much less than BRCA1/2, the distinct mutation spectrum of PALB2 is still obscure. Therefore, we assessed the mutational frequency, spectrum and predictors of the PALB2 gene in a sequential series of Chinese breast cancer patients from our Research DNA Bank, to verify the utility of PALB2 genetic testing in Chinese population. Methods: We examined Chinese breast cancer cases (n = 2279) who agreed to participate in research DNA banking, recruited from 1990 through 2016. To identify the mutations, complete coding sequence and intron–exon boundaries of PALB2 were screened with Next Generation Sequencing. Personal and family histories were synchronously collected for mutation identification. Results: Among the 2279 breast cancer patients, 307 patients were familial breast cancer cases and the rest 1972 patients were sporadic breast cancer cases. PALB2 mutation carriers accounted for 7.8% (n = 24) and 4.8% (n = 95) in familial and sporadic breast cancer cohort separately. In total, 31 missense, 4 nonsense, 3 frameshift, 3 splicing and 1 codon mutations of PALB2 were identified in this study. Among the pathologic variants, PALB2 c.1744C > T, c.2748+1G > A, c.2749-1G > C, c.3114-1G > A were newly identified in sporadic breast cancer, and c.3271delC newly found in familial breast cancer. Based on in silico analysis, a total of 6 potential damaging missense variants were novelly found in this study, among which the PALB2 c.3035C > T was detected in both sporadic and familial breast cancer. Conclusions: Our data presents the germline mutation status of PALB2 in Chinese patients with breast cancer, suggesting that loss-of-function germline mutations of PALB2 are important in both familial and sporadic breast cancer. Clinically, this information may be helpful in genetic counseling of breast cancer patients with PALB2 germline mutation.

Biotechnology for Conservation and Utilization of Agricultural Plant Genetic Resources in Nepal

Agricultural biodiversity is the basis of human life and food security. Nepal with 577 cultivated species possesses huge diversity at varietal as well as landrace levels. In most agricultural crops the rapid genetic erosion due to several reasons is a common phenomenon. Thus, considering the importance of agricultural biodiversity declared by Convention on Biological Diversity for sustainable food production, National Agriculture Genetic Resources Center (NAGRC) has been established for conservation and sustainable utilization of agricultural biodiversity. This paper thus delineates the application of biotechnological tools adopted by NAGRC for effective and efficient conservation and use of agricultural plant genetic resources (APGRs). Among the adopted technologies, tissue bank using shoot tip culture of vegetatively propagating and recalcitrant crops eg potato, sugarcane, banana, sweet potato, etc are in function. Under the molecular marker technology, currently random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers have been used for developing DNA profiles, identifying duplicates in the collections, assessing genetic diversity and screening accessions against economic traits. DNA bank has also been created for storing DNA of indigenous crops and these DNA can be accessed for research and study. Genotypic database has been developed for chayote, finger millet, wheat and maize for identification and selection of the accessions.Journal of Nepal Agricultural Research Council Vol.3 2017: 49-59

A Comparative Study and Survey on Existing DNA Compression Techniques

Data storage and DNA banking are receiving tremendous attention recently, due to the explosion of genetic research, biomedical research and forensic sciences.DNA databases when compared to other databases occupy more storage due to the enormous size of each DNA sequence. They are growing exponentially as newer samples are being collected and stored. This poses a major task for storage, transfer, searching and retrieval of data. Hence,Compression of DNA Databases have become relevant.DNA sequences contain repetitions of A, C, T, G,so compression of the sequence involves searching and encoding these repetitions,then decoding them while decompression.This paper explores a few existing DNA sequence compression algorithmswhich were developed based on certainprevailing generalcompression algorithms. First a few, existing compression techniques are explained and then, fiveavailable DNA sequence compression algorithms are evaluated for their suitability in compressing large collections of DNA sequences. Keywords: DNA, DNA databases, Genetics, DNA compression, Biocompress, Cfact, DNAcompress, Gencompress, CTW+LZ.

BANK OF ANIMAL GENETIC RESOURCES OF INSTITUTE OF ANIMALS BREEDING AND GENETICS ND. A. M.V.ZUBETS OF NAAS SYSTEM OF ANIMAL BIODIVERSITY CONSERVATION OF UKRAINE

BANK OF ANIMAL GENETIC RESOURCES OF INSTITUTE OF ANIMALS BREEDING AND GENETICS ND. A. M.V.ZUBETS OF NAAS SYSTEM OF ANIMAL BIODIVERSITY CONSERVATION OF UKRAINE

Standardization of Long Term DNA Storage and DNA Banking Methods for Conservation of Saudi Date Palm (Phoenix dactylifera L.) Genetic Diversity

Standardization of Long Term DNA Storage and DNA Banking Methods for Conservation of Saudi Date Palm (Phoenix dactylifera L.) Genetic Diversity

Abstract A47: Cancer genetics research in Alabama: Recruitment mechanisms to reach the underserved

Abstract Over 60% of the Alabama population is medically underserved, including the entire population of many Alabama counties. These counties are generally rural and have transportation barriers, thus a lack of access to healthcare results in poor cancer outcomes. These healthcare gaps, in addition to lower education levels and mistrust towards researcher/healthcare providers, highlight the challenges but also the need to make a difference in this underserved and understudied population. In general, recruitment for human genetic research studies presents major challenges, and, despite federal mandates to include women and minorities in federally funded research, African Americans (AAs) remain underrepresented in cancer genetic research. Recruitment of participants requires extensive efforts and strategic planning in order to overcome the difficulties, such as distrust towards medical research and logistical challenges of recruiting under-served and under-represented individuals. These considerations led to the establishment of two IRB-approved protocols, hospital recruitment (#14-232) and community-based recruitment (CBR; #15-111) to recruit cancer individuals/families from Alabama and identify genetic risk factors. Hospital recruitment was established through a partnership with East Alabama Medical Center (EAMC), and CBR targets medically underserved individuals through a mechanism aimed to educate and build trust in the community. Through connections fostered by community-partners, CBR team members travel to rural communities all over Alabama to be introduced to, educate, and recruit patients/survivors and their family members. All CBR team members are phlebotomy trained. Recruitment particularly focuses on cancer associated with Hereditary Breast and Ovarian Cancer (HBOC) Syndrome since there are two disparities within the AA population that may be genetically linked. Firstly, AA women are generally diagnosed with a more aggressive and less treatable breast cancer (BC) sub-type and have a higher incidence rate of BC under the age of 40 compared to Caucasians. Secondly, AA males are generally diagnosed with prostate cancer (PC) at a younger age and with larger tumors compared to Caucasians. Considering that (1) an early age of onset is a hallmark of hereditary cancer, (2) hereditary BC is associated with an increased risk of ovarian cancer (OvC) and PC, and (3) the Black Women's Health Study has demonstrated there is a strong familial component of AA BC, inherited and potentially overlapping genetic risk factors may explain these disparities. Thus, the study enrollment criteria include individuals (1) diagnosed with BC, OvC, or PC under the age of 45 and/or (2) diagnosed with BC, OvC, or PC with have a cancer family history. Ultimately, in an effort to recruit informative families for genetic study, both cancer-affected and unaffected family members of study participants can join the study. To date, 133 DNA samples from 74 cancer families are stored in the Merner DNA Bank; 33 and 41 probands have been recruited through EAMC and CBR, respectively. CBR has been the most effective mechanism of AA BC recruitment (20/36) compared to hospital recruitment (5/32). Probands are screened for known and candidate susceptibility genes using the BRAP (BReast And Prostate) gene-screening panel. This aims to provide insight towards the true contribution of mutations in known susceptibility genes, and identify non-mutation individuals/families for novel HBOC susceptibility gene discovery efforts. Additionally, this study offers each participant the option to receive her/his confidential research-based gene screening results and aims to translate those results to the clinic by providing free UAB telegenetic counseling to underserved individuals through the use of telemedicine carts at equipped Alabama County Health Departments. Citation Format: Nancy Merner, Madison Chandler, Amber Davis, Ebony Jackson, Erin Bilgili, Cameron Turner, Kasey Shepp, Stephanie Spina, Brandon Johnson. Cancer genetics research in Alabama: Recruitment mechanisms to reach the underserved. [abstract]. In: Proceedings of the Ninth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2016 Sep 25-28; Fort Lauderdale, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(2 Suppl):Abstract nr A47.

Friedreich Ataxia: Treatment with Genetic Approach

Friedreich ataxia (FA) is a disorder in the nervous system inherited according to the Mendel’s first law. Mutations in the FXN gene trigger the FA disorder. The FXN gene occupies chromosome 9q21.11 in the chromosome map. Mutations in the FXN gene consist of four classes of alleles. These include normal alleles, changeable normal alleles, complete penetrance alleles, and borderline alleles. Currently, there is no efficient treatment for this disorder. To slow down FA, genetic approach can be used. The approach may comprise genetic counseling and use of gene therapy. In genetic counseling, if both parents are carriers, a child has a 25 % FA. To detect people with carrier, amniocentesis can be used for instance. Preimplantation FA diagnostic can also be made. In gene therapy, DNA banking is needed. It is useful to study Friedreich ataxia for treatment of this disorder. Gene therapy is a method to correct damaged cells of patients. In this article, the author shows viral vectors such as HSV-1 amplicon vectors and lentivirus vectors as gene shipping vehicles. Both can restore the normal point of frataxin. These results show that gene therapy is a promising tool to treat FA disorder.

Biobanking and fertility preservation for rare and endangered species

For more than 25 years, systematic gathering and cryo-storage of biomaterials from diverse wild species have been ongoing to save gene diversity and improve captive (ex situ) and wild (in situ) animal management. Cryo-storage of biomaterials offers broad opportunities - from helping understand the fundamental biology of unstudied species to enhanced conservation breeding, genomics and veterinary medicine. While promoted for decades, the banking of germplasm, tissue, blood and DNA from wildlife species only recently has been considered by some to be a core function of animal conservation programs. Importantly, reproductive biotechnologies and fertility preservation are critical tools for saving and maintaining endangered species and are tightly related to biobanking. Some successes have been reported with the use and integration of artificial insemination (with fresh or frozen-thawed semen) in conservation programs. However, not a single wild species is currently managed through oocyte freezing or embryo-based technologies. This is primarily due to the lack of knowledge of species biology, as well as inadequate facilities, space, expertise, and funding needed for their successful application. More fundamental studies on animal reproductive biology as well as more fertility preservation options are needed with all parties involved (reproductive technologists, zoo biologists and conservationists) adopting parallel efforts to sustain wild populations and habitats

Forensic anthropology in crisis settings: a required component of investigation in the world‘s trouble spots

This article presents an account of the involvement of forensic anthropology in the investigation of human rights abuses in the modern era, and the difficulties it faces with respect to lack of adequate funding, volatile settings, the presence of unexploded ordnance, corruption in governmental agencies and a lack of good will, absence of support for NGOs and the curtailment of formal judicial proceedings to effect transitional justice. Syria, Iraq, Afghanistan, Spain, Mexico and the Northern Triangle are provided as regional examples of the problems encountered when attempting to conduct forensic anthropological investigations to locate mass graves, retrieve victims and obtain proper identifications. Interventions by various organisations are highlighted to illustrate their assistance to forensic and non-forensic individuals through technical support, training and mentoring in the areas of crime-scene management and identification techniques. Interventions in mass-grave processing when state agencies have failed, the importance of DNA banks and information from family members and witnesses are also presented.

ASSOCIATION OF THE MONONUCLEOTIDE POLYMORPHISMS RS62116755 OF GENE GACAT3, RS12170546 OF GENE PARVB, RS16994849 OF GENE PLCB1, RS78143315 OF GENE PDCD6IP WITH SUDDEN CARDIAC DEATH

Aim. To check the association of sudden cardiac death (SCD) with mononucleotide polymorphisms rs62116755 gene GACAT3, rs12170546 gene PARVB, rs16994849 gene PLCB1, rs78143315 gene PDCD6IP, that were set as genetic markers of SCD in previous full-genome associative original study. Material and methods. Group of SCD (n=388, mean age 52,9±9,2 y.o., males — 77,2%, females — 22,8%) was formed by the SCD criteria of World Health Organization and European Society of Cardiology. Controls matched by sex and age (n=387, mean age 52,4±8,8 y.o., males — 62,3%, females — 37,7%) from the DNA banks of international studies MONICA, HAPIEE. Separation of DNA was done with the phenol-chlorophorm extraction. Genotyping was done by polymerase chain reaction with further polymorphism analysis of the lengths of restrictional fragments. Results. There was no association with SCD of the mononucleotide polymorphisms rs62116755 gene GACAT3, rs78143315 gene PDCD6IP. In SCD group the number of TT carriers rs12170546 gene PARVB was significantly lower than in controls (OR =1,66, 95% CI 1,25-2,21, p=0,001; OR =0,67, 95% CI 0,50-0,90, p=0,009, respectively). In the group younger than 50 y.o. the number of GG carriers rs16994849 gene PLCB1 was significantly higher, and of genotype AA — lower, comparing to the controls (OR =4,92, 95% CI 1,01-23,20, p=0,032; OR =0,54, 95% CI 0,31-0,93, p=0,029, respectively). In males older than 50 the part of GG carriers rs16994849 gene PLCB1 was significantly lower than in control group (OR =0,11, 95% CI 0,01-0,91, p=0,024). Conclusion. Mononucleotide polymorphisms rs62116755 gene GACAT3, rs78143315 gene PDCD6IP were not related to SCD. Genotype ТТ of polymorphism rs12170546 gene PARVB is a genotype of risk of SCD, and genotype TC is protective. Genotype GG of polymorphism rs16994849 gene PLCB1 is the genotype of risk for SCD for those younger than 50 y.o. and is protective in those older than 50. Genotype AA of polymorphism rs16994849 gene PLCB1 is protective against SCD in those younger 50 y.o.

Plant DNA banks for genetic resources conservation (review)

Purpose. Literature review of DNA banks creation as the current strategy of plant genetic resources conservation. Results. The current state of plant genetic resources conservation was analyzed in the context of the threat of gene­tic erosion. The importance of DNA banks was shown which function is to store DNA samples and associated products and disseminate them for research purposes. The main DNA banks in the world were described, including the Republican DNA Bank of Human, Animals, Plants and Microorganisms at the Institute of Genetics and Cytology of the National Academy of Sciences of Belarus. Stages of DNA banking were considered: tissue sampling (usually from leaves), cell destruction, DNA extraction, DNA storage. Different methods of tissue sampling, extraction and DNA storage were compared. The need for Plant DNA Bank creation in Ukraine was highlighted. Conclusions. DNA collections is an important resource in the global effort to overcome the crisis in biodiversity, for managing world genetic resources and maximi­zing their potential.

Rare genetic variation in UNC13A may modify survival in amyotrophic lateral sclerosis

Our objective was to identify whether rare genetic variation in amyotrophic lateral sclerosis (ALS) candidate survival genes modifies ALS survival. Candidate genes were selected based on evidence for modifying ALS survival. Each tail of the extreme 1.5% of survival was selected from the UK MND DNA Bank and all samples available underwent whole genome sequencing. A replication set from the Netherlands was used for validation. Sequences of candidate survival genes were extracted and variants passing quality control with a minor allele frequency ≤0.05 were selected for association testing. Analysis was by burden testing using SKAT.Candidate survival genes UNC13A, KIFAP3, and EPHA4 were tested for association in a UK sample comprising 25 short survivors and 25 long survivors. Results showed that only SNVs in UNC13A were associated with survival (p = 6.57 × 10−3). SNV rs10419420:G > A was found exclusively in long survivors (3/25) and rs4808092:G > A exclusively in short survivors (4/25). These findings were not replicated in a Dutch sample. In conclusion, population specific rare variants of UNC13A may modulate survival in ALS.

Abstract 4953: Whole-exome sequencing of single circulating tumor cells according to epithelial-mesenchymal marker expression in metastatic prostate cancer

Abstract Molecular characterization of metastatic castration-resistant prostate cancer (mCRPC) is limited by tumor tissue availability. The analysis of circulating tumor cells (CTCs) offers an attractive non invasive surrogate option to analyze molecular alterations. We report whole exome sequencing (WES) of CTCs at the single cell level in 11 mCRPC patients. We examined single somatic nucleotide variant (sSNV) shared between matched metastatic tumor sample and CTCs and sSNV specific to CTCs. Blood samples were drawn from 11 patients enrolled in the clinical program MOSCATO (2011-A00841-40). CTC enrichment, detection and single cell isolation were performed using three methods to obtain pools of 1-10 CTCs. The first method used ISET filtration, immunofluorescent staining (CD45, pan-cytokeratin, EpCAM, Vimentin and Hoechst 33342) on filters and laser microdissection of single CTCs; the second combined CellSearch and the VyCap puncher system; the third used RosetteSep enrichment, immunofluorescent staining and isolation by cell sorting. Whole Genome Amplification (WGA) was performed using the Ampli1 kit. WGA quality was assessed by qPCR of 7 genes located on different regions of the genome. WES was performed by preparation of a genomic DNA bank, Agilent capture and sequencing on the Illumina HiSeq 2000 platform. Data were aligned to the human genome reference hg19. GATK Haplotype Caller enabled identification of germline polymorphisms from each patient in normal DNA, metastatic sample and CTCs in order to consider WGA induced bias. The detection of sSNV in tumor biopsies and CTCs was assessed with Mutect and IndelGenotyper respectively. 189 WGAs of CTC pools were performed. A first round of WES showed that at least 3 well amplified genes were required to obtain a coverage of at least 50% at 10X depth sequencing. 34 pools of phenotypically different CTCs from 7 patients were selected and sequenced. Mean coverage of 51% was obtained at a sequencing depth of 10X. Allelic drop out was lower for CTC pools containing 5 to 10 cells. 17/34 (50%) CTC samples (4 patients) had shared sSNV with the paired tumor sample (range 0.35%-68%). Epithelial CTCs had more shared sSNV with metastatic biopsies than CTCs of other phenotypes but shared sSNV were also detected in large Cytokeratin-Vimentin- CTC. Shared sSNV in cancer genes between epithelial CTC pools, but not in the paired biopsy, were present in 2 patients. We report WES of CTC pools harboring distinct EMT marker phenotypes is possible with the use of 3 different approaches to enrich, detect and isolate CTCs. The detection of shared sSNV between CTC pools and corresponding biopsy could validate the use of CTCs as a liquid biopsy. The finding of sSNV specific to CTCs could offer additional data on tumor heterogeneity. Ongoing work examining if sSNV detected in phenotypically different CTCs converge to similar signaling pathways will be presented. Citation Format: Vincent Faugeroux, Céline Lefebvre, Emma Pailler, Valérie Pierron, Fanny Billiot, Charles Marcaillou, Philippe Vielh, Semih Dogan, Philippe Rameau, Maud Ngocamus, Jean Charles Soria, Karim Fizazi, Yohann Loriot, Sylvia Julien, Françoise Farace. Whole-exome sequencing of single circulating tumor cells according to epithelial-mesenchymal marker expression in metastatic prostate cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4953.

Prevalence ofMITFp.E318K in Patients With Melanoma Independent of the Presence ofCDKN2ACausative Mutations

The main high-penetrance melanoma susceptibility gene is CDKN2A, encoding p16INK4A and p14ARF. The gene MITF variant p.E318K also predisposes to melanoma and renal cell carcinoma. To date, the prevalence of MITF p.E318K and its clinical and phenotypical implications has not been previously assessed in a single cohort of Spanish patients with melanoma or in p16INK4A mutation carriers. To evaluate the prevalence of MITF p.E318K in Spanish patients with melanoma and assess the association with clinical and phenotypic features. A hospital-based, case-control study was conducted at the Melanoma Unit of Hospital Clinic of Barcelona, with MITF p.E318K genotyped in all patients using TaqMan probes. We included 531 patients: 271 patients with multiple primary melanoma (MPM) without mutations affecting p16INK4A (wild-type p16INK4A); 191 probands from melanoma-prone families with a single melanoma diagnosis and without mutations affecting p16INK4A, and 69 probands from different families carrying CDKN2A mutations affecting p16INK4A. A population-based series of 499 age- and sex-matched cancer-free individuals from the Spanish National Bank of DNA were included as controls. Patients were recruited between January 1, 1992, and June 30, 2014; data analysis was conducted from September 1 to November 30, 2014. The genetic results of the MITF p.E318K variant were correlated with clinical and phenotypic features. Among the 531 patients, the prevalence of the MITF p.E318K variant was calculated among the different subsets of patients included and was 1.9% (9 of 462) in all melanoma patients with wild-type p16INK4A, 2.6% (7 of 271) in those with MPM, and 2.9% (2 of 69) in the probands of families with p16INK4A mutations. With results reported as odds ratio (95% CI), the MITF p.E318K was associated with an increased melanoma risk (3.3 [1.43-7.43]; P < .01), especially in MPM (4.5 [1.83-11.01]; P < .01) and high nevi count (>200 nevi) (8.4 [2.14-33.19]; P < .01). Two fast-growing melanomas were detected among 2 MITF p.E318K carriers during dermatologic digital follow-up. In addition to melanoma risk, MITF p.E318K is associated with a high nevi count and could play a role in fast-growing melanomas. Testing for MITF p.E318K should not exclude patients with known mutations in p16INK4A. Strict dermatologic surveillance, periodic self-examination, and renal cell carcinoma surveillance should be encouraged in this context.

Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer.

Testing for germline mutations in BRCA1/2 is standard for select patients with breast cancer to guide clinical management. Next-generation sequencing (NGS) allows testing for mutations in additional breast cancer predisposition genes. The frequency of germline mutations detected by using NGS has been reported in patients with breast cancer who were referred for BRCA1/2 testing or with triple-negative breast cancer. We assessed the frequency and predictors of mutations in 25 cancer predisposition genes, including BRCA1/2, in a sequential series of patients with breast cancer at an academic institution to examine the utility of genetic testing in this population. Patients with stages I to III breast cancer who were seen at a single cancer center between 2010 and 2012, and who agreed to participate in research DNA banking, were included (N = 488). Personal and family cancer histories were collected and germline DNA was sequenced with NGS to identify mutations. Deleterious mutations were identified in 10.7% of women, including 6.1% in BRCA1/2 (5.1% in non-Ashkenazi Jewish patients) and 4.6% in other breast/ovarian cancer predisposition genes including CHEK2 (n = 10), ATM (n = 4), BRIP1 (n = 4), and one each in PALB2, PTEN, NBN, RAD51C, RAD51D, MSH6, and PMS2. Whereas young age (P < .01), Ashkenazi Jewish ancestry (P < .01), triple-negative breast cancer (P = .01), and family history of breast/ovarian cancer (P = .01) predicted for BRCA1/2 mutations, no factors predicted for mutations in other breast cancer predisposition genes. Among sequential patients with breast cancer, 10.7% were found to have a germline mutation in a gene that predisposes women to breast or ovarian cancer, using a panel of 25 predisposition genes. Factors that predict for BRCA1/2 mutations do not predict for mutations in other breast/ovarian cancer susceptibility genes when these genes are analyzed as a single group. Additional cohorts will be helpful to define individuals at higher risk of carrying mutations in genes other than BRCA1/2.

Digitotalar dysmorphism: Molecular elucidation.

Dominantly inherited digitotalar dysmorphism (DTD), which is characterised by flexion contractures of digits and 'rocker-bottom' feet due to a vertical talus, was first described in a South African family of European stock in 1972. We review the clinical manifestations and document the molecular basis for DTD in this prototype family. This family was restudied in 1995 and 2006 and biological specimens were obtained for molecular studies. Since the distal arthrogryposes (DAs) are genetically heterogeneous, an unbiased approach to mutation identification was undertaken through whole-exome next-generation sequencing of DNA from a single DTD-affected female. Venous blood specimens were obtained for DNA banking and subsequent molecular studies. Analysis of the nine genes that had previously been shown to cause DAs revealed a pathogenic mutation in exon nine of TNNT3. The presence of the p.(Arg63His) missense mutation at position 63 of TNNT3 was confirmed through direct cycle sequencing of genomic DNA in six affected family members for whom DNA had been archived.

A computer-assisted method for pathogenicity assessment and genetic reporting of variants stored in the Australian Inherited Retinal Disease Register.

The assignment of pathogenicity to variants suspected of causing an inherited retinal disease and the subsequent creation of molecular genetic reports sent to clinical geneticists and ophthalmologists has traditionally been time-consuming and subject to error and ambiguity. The purpose of this paper is to describe a computer-assisted method we have developed for (1) assessment of the predicted pathogenicity of genetic variants identified in patients diagnosed with an inherited retinal disease and (2) the incorporation of these results into the Australian Inherited Retinal Disease Register and DNA Bank's databases, for the production of molecular genetics reports. This method has significantly accelerated the assessment of variant pathogenicity prediction and subsequent patient report generation for the Australian Inherited Retinal Disease Register and DNA Bank, and has reduced the potential for human error. The principles described in this paper may be applied in any situation where genetic variants and patient information are stored in a well-organised database.

Novel ALOX12B Mutation Identified in Parents following Single Nucleotide Polymorphism Microarray Testing of Banked DNA from a Fatal Case of Congenital Ichthyosis.

In genetically and phenotypically heterogeneous conditions like ichthyosis, it is clinically not possible to predict mutation in a specific gene. Sequential testing of all the causative genes is time consuming and expensive. In consanguineous families with autosomal recessive genetically heterogeneous disorders, it is possible to narrow down the candidate gene/genes by recognizing the regions of homozygosity by a single nucleotide polymorphism (SNP) array. Here, we present a fatal case of autosomal recessive severe congenital ichthyosis born to a consanguineous couple. Two candidate genes were recognized by SNP array on banked DNA of the subject. Sequencing of these candidate genes in parents found them to be carriers of the same variation, a novel heterozygous deletion of single nucleotide in exon 8 (c. 1067delT) of ALOX12B gene. The present case illustrates the utility of DNA banking, SNP array and testing of parents to arrive at a definitive molecular diagnosis, essential for genetic counseling, and prenatal testing.