Our understanding of the molecular classification of colorectal carcinoma (CRC) has evolved significantly over the past two decades. Tumours can be broadly categorised as microsatellite stable (MSS), microsatellite instability (MSI) or CpG island-methylator phenotype. Prognostic and predictive information is provided by these categories. The overwhelming majority of the data on which these categories are based have originated from Europe and North America. There is a dearth of information represented from Africa and indigenous African patients. However, some small studies and preliminary data have shown significant differences in all of these groups. The prevalence of MSI in Africa is consistently reported as almost double that of European and North American data. Interestingly, BRAF V600E mutations and MLH1 promotor hypermethylation seem to be uncommon in Africa. The high proportion of MSI tumours is only partly accounted for by germline mutations in mismatch repair genes (Lynch syndrome), suggesting that there are likely to be other mechanisms at play. Within the MSS group, preliminary data suggest that the typical molecular pathways (Wingless/Integrated pathway activation) may not be as dominant in Africa. The purpose of this review is to summarise the current state of the molecular genetic landscape of CRC in Africa and provide insights into areas for further study.

Epilepsy in Africa Sub-Saharan Africa (SSA) carries the greatest burden of epilepsy in the world, exacerbated by the high incidence of central nervous system infections, perinatal insults and traumatic brain injury. [1] Almost 60% of people with epilepsy in SSA do not receive medication, and only about a third of those who do are appropriately managed.[2] The substantial risk of premature mortality associated with epilepsy in Africa (22.2 45.1 per 1 000[3]) is strongly linked to poor seizure control. Reduced access to education and employment opportunities, as well as the social stigma attached to epilepsy in some communities, all place a burden on the individual and the family. The period of infancy carries the highest incidence of epilepsy,[4] with some of the worst immediate and long-term sequelae affecting all areas of the infants’ and their carers’ lives. Early diagnosis and correct management are critical in mitigating the detrimental effects of uncontrolled seizures on the maturing brain.[5] Most epilepsies previously termed ‘idiopathic’ (i.e. without a clear acquired cause) have a genetic basis.[6] The advent of nextgeneration sequencing (NGS) created a massive surge in epilepsy gene discovery, revealing a previously unappreciated genetic and phenotypic heterogeneity. Over 350 genes have been associated with epilepsy to date,[7] with a remarkably high frequency of de novo variants, especially among the developmental and epileptic encephalopathies (DEEs)[8]. Large-scale studies continue to expand and refine the phenotypic spectrum of known epilepsy-associated genes, with certain clinical features linked to variants in specific genes.[9] Examples include movement disorders and head stereotypies in STXBP1-related DEE,[10] and clustered focal seizures restricted to females with PCDH19 variants.[11] The genetic and phenotypic heterogeneity of epilepsy is exemplified by the SCN1A seizure disorders, where SCN1A variants may cause a severe, drug-resistant DEE (Dravet syndrome (DS))[12] in some patients, or milder disease in others (e.g. generalised epilepsy with febrile seizures plus (GEFS+)). [13] The precise determinants of this heterogeneity are still unknown, but somatic mosaicism and functional effects of specific variants are known to play a role.[14] Importantly, knowledge of the causative mutation may guide the choice of treatment. Examples of precision therapies include the ketogenic diet for glucose transporter deficiency (SLC2A1), phenytoin or high-dose carbamazepine for SCN2A and SCN8A, and avoidance of sodium channel blockers in SCN1A-related epilepsy.[15] Genetic testing for epilepsy is now firmly embedded in the diagnostic setting of high-income counties (HICs), particularly for the DEEs, where the rate of informative findings is highest, with a demonstrable utility and cost benefit.[16,17] A recent global burden of disease report ranked ‘idiopathic epilepsy’ (epilepsy of genetic origin or without a definite structural, metabolic, infective or immune cause) as the second most common neurological disorder in southern SSA.[18] Yet little is known about the genetic architecture of epilepsy in SSA, and no genetic testing is available locally.[19] While local research may uncover new genes and variants, it is likely that the genetic aetiology of de novo epilepsies in Africa is similar to the HICs. Research and translation in this instance should therefore happen almost simultaneously. Unfortunately, the expense of genomic analysis is a major limitation, as the anticipated reduction in NGS cost has not materialised tangibly in Africa. Suppliers base price negotiations on projected throughput, which is difficult in a setting of limited budget for genetic services, particularly in a state sector overwhelmed by the burden of infectious diseases. Paradoxically, it is often cheaper to refer NGS analyses abroad than to test locally, which presents an economical solution initially but does not serve to build local capacity. The shortage of suitably qualified workforce could be remedied by investment in training and creative use of the existing infrastructure, but requires buy-in and financial support from the health authorities.

RPGRexon ORF15 variants are one of the most frequent causes for inherited retinal disorders (IRDs), in particular retinitis pigmentosa. The low sequence complexity of this mutation hotspot makes it prone to indels and challenging for sequence data analysis. Whole-exome sequencing generally fails to provide adequate coverage in this region. Therefore, complementary methods are needed to avoid false positives as well as negative results. In this study, next-generation sequencing (NGS) was used to sequence long-range PCR amplicons for an IRD cohort of African ancestry. By developing a novel secondary analysis pipeline based on de novo assembly, we were able to avoid the miscalling of variants generated by standard NGS analysis tools. We identified pathogenic variants in 11 patients (13% of the cohort), two of which have not been reported previously. We provide a novel and alternative end-to-end secondary analysis pipeline for targeted NGS of ORF15 that is less prone to false positive and negative variant calls.

PURPOSE:Dravet syndrome (DS) is a well-described, severe genetic epileptic encephalopathy with an increased risk of SUDEP. The incidence and genetic architecture of DS in African patients is virtually unknown, largely due to lack of awareness and unavailability of genetic testing. The clinical benefits of the available precision medicine approaches to treatment emphasise the importance of an early, correct diagnosis. We investigated the genetic causes and clinical features of DS in South African children to develop protocols for early, cost-effective diagnosis in the local setting.METHOD:We selected 22 South African children provisionally diagnosed with clinical DS for targeted resequencing of DS-associated genes. We sought to identify the clinical features most strongly associated with SCN1A-related DS, using the DS risk score and clinical co-variates under various statistical models.RESULTS:Disease-causing variants were identified in 10 of the 22 children: nine SCN1A and one PCDH19. Moreover, we showed that seizure onset before 6 months of age and a clinical DS risk score of >6 are highly predictive of SCN1A-associated DS. Clinical reassessment resulted in a revised diagnosis in 10 of the 12 variant-negative children.CONCLUSION:This first genetic study of DS in Africa confirms that de novo SCN1A variants underlie disease in the majority of South African patients. Affirming the predictive value of seizure onset before 6 months of age and a clinical DS risk score of >6 has significant practical implications for the resource-limited setting, presenting simple diagnostic criteria which can facilitate early correct treatment, specialist consultation and genetic testing.

Spondyloepimetaphyseal dysplasia with joint laxity (SEMDJL) is an autosomal-recessive skeletal dysplasia. A relatively large number of patients with SEMDJL have been identified in the Caucasian Afrikaans-speaking community in South Africa. We used a combination of Genome-Wide Human Single Nucleotide Polymorphism (SNP) Array 6.0 data and whole exomic data to potentially dissect genetic modifiers associated with SEMDJL in Caucasian Afrikaans-speaking patients. Leveraging the family-based association signal in prioritizing candidate mutations, we identified two potential modifier genes, COL1A2 and MATN1, and replicating previously identified mutation in KIF22. Importantly, our findings of genetic modifier genes and previously identified mutations are layered on the same sub-network implicated in syndromes characterized by skeletal abnormalities and intellectual disability, bone and connective tissue fragility. This study has potentially provided crucial insights in identifying the indirect modifying mutation(s) linked to the true causal mutation associated with SEMDJL. It is a critical lesson that one may use constructively especially when the pace of exomic sequencing of rare disorders continues apace.

Background: There have been considerable recent advances in understanding the genetic architecture of anxiety disorders and posttraumatic stress disorder (PTSD), as well as the underlying neurocircuitry of these disorders. However, there is little work on the concordance of genetic variations that increase risk for these conditions, and that influence subcortical brain structures. We undertook a genome-wide investigation of the overlap between the genetic influences from single nucleotide polymorphisms (SNPs) on volumes of subcortical brain structures and genetic risk for anxiety disorders and PTSD. Method: We obtained summary statistics of genome-wide association studies (GWAS) of anxiety disorders (N-cases = 7016, N-controls = 14,745), PTSD (European sample; N-cases = 2424, N-controls = 7113) and of subcortical brain structures (N = 13,171). SNP Effect Concordance Analysis (SECA) and Linkage Disequilibrium (LD) Score Regression were used to examine genetic pleiotropy, concordance, and genome-wide correlations respectively. SECAs conditional false discovery was used to identify specific risk variants associated with anxiety disorders or PTSD when conditioning on brain related traits. Results: For anxiety disorders, we found evidence of significant concordance between increased anxiety risk variants and variants associated with smaller amygdala volume. Further, by conditioning on brain volume GWAS, we identified novel variants that associate with smaller brain volumes and increase risk for disorders: rs56242606 was found to increase risk for anxiety disorders, while two variants (rs6470292 and rs683250) increase risk for PTSD, when conditioning on the GWAS of putamen volume. Limitations: Despite using the largest available GWAS summary statistics, the analyses were limited by sample size. Conclusions: These preliminary data indicate that there is genome wide concordance between genetic risk factors for anxiety disorders and those for smaller amygdala volume, which is consistent with research that supports the involvement of the amygdala in anxiety disorders. It is notable that a genetic variant that contributes to both reduced putamen volume and PTSD plays a key role in the glutamatergic system. Further work with GWAS summary statistics from larger samples, and a more extensive look at the genetics underlying brain circuits, is needed to fully delineate the genetic architecture of these disorders and their underlying neurocircuitry.

Over 80% of people with epilepsy live in low- to middle-income countries where epilepsy is often undiagnosed and untreated due to limited resources and poor infrastructure. In Africa, the burden of epilepsy is exacerbated by increased risk factors such as central nervous system infections, perinatal insults, and traumatic brain injury. Despite the high incidence of these etiologies, the cause of epilepsy in over 60% of African children is unknown, suggesting a possible genetic origin. Large-scale genetic and genomic research in Europe and North America has revealed new genes and variants underlying disease in a range of epilepsy phenotypes. The relevance of this knowledge to patient care is especially evident among infants with early-onset epilepsies, where early genetic testing can confirm the diagnosis and direct treatment, potentially improving prognosis and quality of life. In Africa, however, genetic epilepsies are among the most under-investigated neurological disorders, and little knowledge currently exists on the genetics of epilepsy among African patients. The increased diversity on the continent may yield unique, important epilepsy-associated genotypes, currently absent from the North American or European diagnostic testing protocols. In this review, we propose that there is strong justification for developing the capacity to offer genetic testing for children with epilepsy in Africa, informed mostly by the existing counseling and interventional needs. Initial simple protocols involving well-recognized epilepsy genes will not only help patients but will give rise to further clinically relevant research, thus increasing knowledge and capacity.

BackgroundPrevious epidemiological studies investigating modification of organophosphate (OP) neurotoxicity by xenobiotic metabolizing enzymes (XMEs) polymorphisms have produced inconsistent results. MethodsA cross-sectional study of 301 emerging farmers was conducted. Neurotoxicity testing included forward and backward recall, digit span, and vibration sensitivity testing. Questionnaire data included demography, potential confounders, and work history of pesticide exposures. Genomic DNA was analyzed from study participants for DNA variants of two glutathione S-transferases (GSTM1 and GSTT1), N-acetyltransferase 2 (NAT2), and Paraoxonase 1 (PON1). ResultsThere was evidence of OP pesticide neurotoxicity modification by rs1799931 (NAT2), rs662 (PON1), and the null allele of GSTM1 in multivariate analysis. The strongest evidence of modification was observed for rs1799931 (NAT2) on the relationship between pesticide poisoning and impaired vibration sense. ConclusionsDNA variants of NAT2, PON1, and GSTM1 may modify OP neurotoxicity, and this requires further exploration.

International Journal of CancerVolume 138, Issue 4 p. 1033-1034 Letter to the EditorFree Access Toward colorectal cancer control in Africa Adeyinka O. Laiyemo, Corresponding Author Adeyinka O. Laiyemo Division of Gastroenterology, Department of Medicine, Howard University College of Medicine, Washington, D.C.Correspondence to: Adeyinka O. Laiyemo, M.D., M.P.H., Division of Gastroenterology, Department of Medicine, Howard University College of Medicine, 2041 Georgia Avenue, NW, Washington DC 20060, USA, Tel.: (202) 865-7186, Fax: (202) 865-4607, E-mail: adeyinka.laiyemo@howard.eduSearch for more papers by this authorOtis Brawley, Otis Brawley American Cancer Society, Atlanta, GASearch for more papers by this authorDavid Irabor, David Irabor Department of Surgery, University of Ibadan, Ibadan, NigeriaSearch for more papers by this authorAdam Boutall, Adam Boutall Groote Schuur Hospital, Cape Town, South AfricaSearch for more papers by this authorRajkumar S. Ramesar, Rajkumar S. Ramesar UCT/SA MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South AfricaSearch for more papers by this authorThandinkosi E. Madiba, Thandinkosi E. Madiba Department of Surgery, University of KwaZulu-Natal, KwaZulu-Natal, South AfricaSearch for more papers by this author Adeyinka O. Laiyemo, Corresponding Author Adeyinka O. Laiyemo Division of Gastroenterology, Department of Medicine, Howard University College of Medicine, Washington, D.C.Correspondence to: Adeyinka O. Laiyemo, M.D., M.P.H., Division of Gastroenterology, Department of Medicine, Howard University College of Medicine, 2041 Georgia Avenue, NW, Washington DC 20060, USA, Tel.: (202) 865-7186, Fax: (202) 865-4607, E-mail: adeyinka.laiyemo@howard.eduSearch for more papers by this authorOtis Brawley, Otis Brawley American Cancer Society, Atlanta, GASearch for more papers by this authorDavid Irabor, David Irabor Department of Surgery, University of Ibadan, Ibadan, NigeriaSearch for more papers by this authorAdam Boutall, Adam Boutall Groote Schuur Hospital, Cape Town, South AfricaSearch for more papers by this authorRajkumar S. Ramesar, Rajkumar S. Ramesar UCT/SA MRC Human Genetics Research Unit, Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South AfricaSearch for more papers by this authorThandinkosi E. Madiba, Thandinkosi E. Madiba Department of Surgery, University of KwaZulu-Natal, KwaZulu-Natal, South AfricaSearch for more papers by this author First published: 10 September 2015 https://doi.org/10.1002/ijc.29843Citations: 13AboutSectionsPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat Colorectal cancer (CRC) is a malignancy with a relatively long preclinical phase which provides a unique opportunity for screening and early detection. Many developed countries have either established programmatic CRC screening endeavors or use healthcare systems that can facilitate early detection and treatment of CRC. The story is quite different in continental Africa. Although the burden of CRC is relatively lower in most countries in Africa when compared to developed countries, there is very little investment in CRC control. There is a general lack of CRC screening programs and poor access to standard treatment for this disease. Under the auspices of the African Organization for Research and Training in Cancer (AORTIC), the challenges and possible solutions to enhance CRC control were discussed at the 9th scientific meeting of the organization in Durban, South Africa in November 2013. The major challenges to CRC control include patient factors such as low socioeconomic status and health literacy which lead to patronage of unstandardized alternative medical care including traditional practices and religious (faith) healing; and health system factors such as lack of effective health insurance systems which promotes cash-based healthcare delivery. There is a lack of adequate manpower of cancer control experts from prevention to treatment of diseases. Furthermore, there is a constant inadequate budget for health by various governments in Africa. Therefore, increasing available resources, equipment, facilities and healthcare providers such as gastroenterologists, surgeons, radiation oncologists and oncology nurses will be essential. Although inadequate research opportunities and data collection systems raise concerns of possible under-reporting, available data suggest a lower burden of CRC in Africa.1 While the overwhelming majority of the population in Africa is of indigenous African origin (black), countries with substantial other racial groups, such as in South Africa, report significant population (racial) differences in CRC burden. The lowest burden of disease have been noted among blacks, and especially those who have maintained their traditional lifestyle including diet, an intermediate burden among Indians and those of mixed ancestry (coloreds) and the highest burden among persons of European origin (whites).1 This contrasts the findings in the United States where African Americans suffer a disproportionally higher burden of CRC when compared to other population groups.2 Of note, there is no organized population-based CRC screening in any African country. Characterization of familial and genetic predisposition to CRC has not been carried out at the population level in Africa. This highlights the need to improve education and access to genetic testing in Africa. In rural communities in South Africa, mobile colonoscopic screening of high-risk patients with mismatch repair gene defects has been shown to improve survival.3 In this mobile screening endeavor, once patients are diagnosed with a cancer, they are referred to a dedicated colorectal unit. Primary prevention of CRC is needed to mitigate expected rise in the burden of the disease in Africa as more people adopt Western lifestyle and dietary patterns. This will involve stellar health promotion on a national scale in every African country to improve awareness and reduce the stigma and taboo associated with cancer. Primary prevention strategies including healthy living, avoiding cigarette smoking, maintaining healthy weight and CRC screening should be encouraged. Given the cost and lack of adequate capacity for colonoscopy in virtually all African countries, an initial targeted CRC screening may be instituted. This will involve screening of family members of an index patient with CRC diagnosis, especially focusing on those diagnosed under the age of 50 years. They should be screened with colonoscopy or fecal immunochemical tests as resources permit. Of note, Quintero et al.4 reported, in a recent study, that yearly fecal immunochemical tests over the three-year duration of the study was not inferior to colonoscopy in detecting advanced colorectal neoplasia among first degree relatives of patients with CRC. The initial modality for opportunistic and programmatic screening for the general, average risk population should be with stool-based tests with follow-up colonoscopy for abnormal results. This is due to the proven efficacy, relatively lower cost and lack of adequate capacity for endoscopy-based screening modalities. It will be important to conduct population-based research to establish the most cost effective and culturally acceptable approach to population-based screening in Africa. Mathematical modeling may also be informative with reasonable assumptions based on the unique characteristics of the population. Given the projection that Africa will have an 85% increase in cancer burden in the next 15 years (by 2030), it is imperative that certain steps be undertaken to reduce the burden of CRC or at least slow down the expected rise in the disease burden.5 The suggested steps include: Build a strong private–public relationship to ensure optimal allocation of resources devoted to cancer control and establish cancer registries to ensure adequate cataloging of disease burden. Increase health literacy campaign to engage the population on the signs and symptoms suggestive of CRC and encourage discussions about cancer in the community. Identify high-risk groups (those with predisposing genetic diseases such as Familial Adenomatous Polyposis (FAP), Lynch syndrome, those with first degree relatives with CRC and those with inflammatory bowel disease); and encourage family discussions about CRC and screening for the disease. Establish regional cancer centers to serve the population and maximize the reach of limited resources, and Begin CRC screening and early detection targeting family members of patients with CRC diagnosis. In conclusion, there is a need to improve communal education and awareness about cancers in general, and CRC in particular in Africa. Private–Public–Partnership investments would be essential to address known barriers to establishing durable CRC screening programs in Africa. Further discussions and strategic planning to improve CRC control will continue at the 10th scientific meeting of AORTIC scheduled to take place in Marrakech, Morocco from November 18–22, 2015. The theme of AORTIC 2015 is “Roadmap to Cancer Control in Africa” and this international conference on cancer will focus on all aspects of cancer management from prevention and early diagnosis, to treatment and palliation. Acknowledgement Dr. Laiyemo is supported by grant awards from the National Center for Advancing Translational Science, (Grant: KL2TR000102-04 and UL1RT000101) and from the National Institute for Diabetes, Digestive Diseases and Kidney (Grant: R21DK100875), National Institutes of Health. References 1Graham A, Adeloye D, Theodoratou LG, et al. Estimating the incidence of colorectal cancer in Sub-Saharan Africa: A systematic analysis. J Glob Health 2012; 2: 020404. 2Siegel RL, Miller KD, Jemal A. Cancer statistics, 2015. CA Cancer J Clin 2015; 65: 5– 29. 3Stupart DA, Goldberg PA, Algar U, et al. Surveillance colonoscopy improves survival in a cohort of subjects with a single mismatch repair gene mutation. Colorectal Dis 2009; 11: 126– 30. 4Quintero E, Carrillo M, Gimeno-García AZ, et al. Equivalency of fecal immunochemical tests and colonoscopy in familial colorectal cancer screening. Gastroenterology 2014; 147: 1021– 30. 5Morhason-Bello IO, Odedina F, Rebbeck TR, et al. Challenges and opportunities in cancer control in Africa: a perspective from the African Organisation for Research and Training in Cancer. Lancet Oncol 2013; 14: e142– e151. Citing Literature Volume138, Issue415 February 2016Pages 1033-1034 ReferencesRelatedInformation

BACKGROUND:Beukes hip dysplasia (BHD) is an autosomal dominant disorder of variable penetrance that was originally identified in a large South African family of European origin. BHD is characterised by bilateral dysmorphism of the proximal femur, which results in severe degenerative osteoarthropathy. Previous studies mapped the disorder to a 3.34 Mb region on chromosome 4q35.OBJECTIVE:To fine-map the BHD locus and identify the disease-causing mutation by direct sequencing.RESULTS:The linked BHD allele was refined to 1.33 Mb, reducing the number of candidate genes from 25 to 16. Analysis of protein coding and invariant splice-site sequences in three distantly related individuals identified a single-candidate disease-causing variant c.868T>C within exon 8 of the ubiquitin-fold modifier 1 (Ufm1)-specific peptidase 2 gene, UFSP2. The presence of this unique mutation was confirmed in all 17 affected members of the BHD family who were genotyped. The mutation segregated with the BHD phenotype in the extended family with a two-point (single marker) LOD score of 10.4 (θ=0.0 and 80% penetrance). The mutation predicts the substitution of a highly conserved amino acid, p.Tyr290His, in the encoded protein. In vitro functional assays performed using purified recombinant wild-type and mutant UFSP2 protein demonstrated that the BHD mutation abolishes UFSP2-mediated C-terminal cleavage of its substrate, Ufm1.CONCLUSION:We report a unique UFSP2 mutation that segregates with the BHD phenotype. The predicted amino acid substitution inactivates UFSP2 proteolytic function, thus implicating the ubiquitin-fold modifier 1 cascade in this form of severe hip osteoarthropathy. The facile polymerase chain reaction-based assay we describe could be used to confirm the diagnosis of BHD, or for presymptomatic testing of members of the extended BHD family.

We report a study of genome-wide, dense SNP (∼900K) and copy number polymorphism data of indigenous southern Africans. We demonstrate the genetic contribution to southern and eastern African populations, which involved admixture between indigenous San, Niger-Congo-speaking and populations of Eurasian ancestry. This finding illustrates the need to account for stratification in genome-wide association studies, and that admixture mapping would likely be a successful approach in these populations. We developed a strategy to detect the signature of selection prior to and following putative admixture events. Several genomic regions show an unusual excess of Niger-Kordofanian, and unusual deficiency of both San and Eurasian ancestry, which were considered the footprints of selection after population admixture. Several SNPs with strong allele frequency differences were observed predominantly between the admixed indigenous southern African populations, and their ancestral Eurasian populations. Interestingly, many candidate genes, which were identified within the genomic regions showing signals for selection, were associated with southern African-specific high-risk, mostly communicable diseases, such as malaria, influenza, tuberculosis, and human immunodeficiency virus/AIDs. This observation suggests a potentially important role that these genes might have played in adapting to the environment. Additionally, our analyses of haplotype structure, linkage disequilibrium, recombination, copy number variation and genome-wide admixture highlight, and support the unique position of San relative to both African and non-African populations. This study contributes to a better understanding of population ancestry and selection in south-eastern African populations; and the data and results obtained will support research into the genetic contributions to infectious as well as non-communicable diseases in the region.

Biallelic germline mutations in mismatch repair genes predispose to constitutional mismatch repair deficiency syndrome (CMMR-D). The condition is characterized by a broad spectrum of early-onset tumors, including hematological, brain and bowel and is frequently associated with features of Neurofibromatosis type 1. Few definitive screening recommendations have been suggested and no published reports have described predictive testing. We report on the first case of predictive testing for CMMR-D following the identification of two non-consanguineous parents, with the same heterozygous mutation in MLH1: c.1528C > T. The genetic counseling offered to the family, for their two at-risk daughters, is discussed with a focus on the ethical considerations of testing children for known cancer-causing variants. The challenges that are encountered when reporting on heterozygosity in a child younger than 18 years (disclosure of carrier status and risk for Lynch syndrome), when discovered during testing for homozygosity, are addressed. In addition, the identification of CMMR-D in a three year old, and the recommended clinical surveillance that was proposed for this individual is discussed. Despite predictive testing and presymptomatic screening, the sudden death of the child with CMMR-D syndrome occurred 6 months after her last surveillance MRI. This report further highlights the difficulty of developing guidelines, as a result of the rarity of cases and diversity of presentation.

Genetic anticipation is the phenomenon in which age of onset of an inherited disorder decreases in successive generations. Inconsistent evidence suggests that this occurs in Lynch syndrome. A possible cause for apparent anticipation is fecundity bias, which occurs if the disease adversely affects fertility. The purpose of this study was to determine the effect of age of diagnosis of colorectal cancer (CRC) on lifetime fertility in Lynch syndrome, and whether this can falsely create the appearance of genetic anticipation. A computer model simulated age of diagnosis of CRC in hypothetical Lynch syndrome carriers and their offspring. The model assumed similar age distribution of CRC across generations (i.e. that there was no true anticipation). Age distribution of CRC diagnosis, and lifetime fertility rates (grouped by age of diagnosis of CRC) were determined from the Australasian Colorectal Cancer Family Registry (ACCFR). Apparent anticipation was calculated by comparing ages of diagnosis of CRC in affected parent–child pairs. A total of 1,088 patients with CRC were identified from the ACCFR. Total lifetime (cohort) fertility was related to age of diagnosis of CRC (correlation coefficient 0.13, P = 0.0001). In the simulation, apparent anticipation was 1.8 ± 0.54 years (P = 0.0044). Observed apparent anticipation in the ACCFR cohort was 4.8 ± 1.73 years (P = 0.0064). There was no difference in apparent anticipation between the simulate d and observed parent–child pairs (P = 0.89). The appearance of genetic anticipation in Lynch syndrome can be falsely created due to changes in fertility.

BACKGROUND:Ototoxicity is an adverse drug reaction that may limit the effective use of cisplatin chemotherapy. Given the reported in vitro protective role of the gene Otos in response to cisplatin, this study aimed to explore the potential of Otos as a genetic modifier of ototoxicity.PATIENTS & METHODS:One hundred South African cisplatin-receiving cancer patients with baseline and follow-up audiometric data were screened for variation in exonic target regions of Otos using direct cycle sequencing.RESULTS:A total of 29 genetic variants were identified. The G alleles of Otos rs77124181 (c.-192-182C>G) and rs2291767 (c.-192-22A>G) were over-represented in ototoxicity-free patients (p = 0.022). Cumulative cisplatin dose and anatomical site of cancer were also associated with ototoxicity, while self-reported ethnicity associated with the ototoxic severity.CONCLUSION:This study indicates a potentially protective role for the variant G alleles of SNPs rs77124181 and rs2291767 in Otos against the development of cisplatin-induced ototoxicity.

Alcohol dependence (AD) has a large heritable component. Genetic variation in genes involved in the absorption and elimination of ethanol have been associated with AD. However, some of these polymorphisms are not present in an African population. Previous studies have reported that a type of AD which is characterized by anxious behaviour may be a genetically specific subtype of AD. We investigated whether variation in genes encoding cytochrome P450 2E1 (CYP2E1) or acetaldehyde-metabolising enzymes (ALDH1A1, ALDH2) might alter the risk of AD, with and without symptoms of anxiety, in a Cape population with mixed ancestry. Eighty case control pairs (one with AD, one without AD) were recruited and individually matched for potential confounders. Genotype data were available for 29 single-nucleotide polymorphisms (SNPs) across the three genes. Linkage disequilibrium D′ values were evaluated for all pairwise comparisons. Allele and haplotype frequencies were compared between cases and controls using a χ 2 test. The ACAG haplotype in block 4 of the ALDH1A1 gene provided evidence of an association with AD (p = 0.03) and weak evidence of an association with AD without symptoms of anxiety (p = 0.06). When a genetic score was constructed using SNPs showing nominal evidence of association with AD, every extra risk allele increased the odds of AD by 35 % (OR 1.35, 95%CI 1.08, 1.68, p = 0.008) and the odds of having AD with anxiety symptoms increased by 53 % (OR 1.53, 95%CI 1.14, 2.05, p = 0.004). Although our results are supported by previous studies in other populations, they must be interpreted with caution due to the small sample size and the potential influence of population stratification.

Stargardt disease is an ABCA4 -associated retinopathy, which generally follows an autosomal recessive inheritance pattern and is a frequent cause of macular degeneration in childhood. ABCA4 displays significant allelic heterogeneity whereby different mutations can cause retinal diseases with varying severity and age of onset. A genotype–phenotype model has been proposed linking ABCA4 mutations, purported ABCA4 functional protein activity and severity of disease, as measured by degree of visual loss and the age of onset. It has, however, been difficult to verify this model statistically in observational studies, as the number of individuals sharing any particular mutation combination is typically low. Seven founder mutations have been identified in a large number of Caucasian Afrikaner patients in South Africa, making it possible to test the genotype–phenotype model. A generalised linear model was developed to predict and assess the relative pathogenic contribution of the seven mutations to the age of onset of Stargardt disease. It is shown that the pathogenicity of an individual mutation can differ significantly depending on the genetic context in which it occurs. The results reported here may be used to identify suitable candidates for inclusion in clinical trials, as well as guide the genetic counselling of affected individuals and families.

The clinical classification of hereditary sequence variants identified in disease-related genes directly affects clinical management of patients and their relatives. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) undertook a collaborative effort to develop, test and apply a standardized classification scheme to constitutional variants in the Lynch syndrome-associated genes MLH1, MSH2, MSH6 and PMS2. Unpublished data submission was encouraged to assist in variant classification and was recognized through microattribution. The scheme was refined by multidisciplinary expert committee review of the clinical and functional data available for variants, applied to 2,360 sequence alterations, and disseminated online. Assessment using validated criteria altered classifications for 66% of 12,006 database entries. Clinical recommendations based on transparent evaluation are now possible for 1,370 variants that were not obviously protein truncating from nomenclature. This large-scale endeavor will facilitate the consistent management of families suspected to have Lynch syndrome and demonstrates the value of multidisciplinary collaboration in the curation and classification of variants in public locus-specific databases.

Bryony A. Thompson, Amanda B. Spurdle, John-Paul Plazzer, Marc S. Greenblatt, Kiwamu Akagi, Fahd Al-Mulla, Bharati Bapat, Inge Bernstein, Gabriel Capellá, Johan den Dunnen, Desiree du Sart, Aurelie Fabre, Michael P. Farrell, Susan M. Farrington, Ian M. Frayling, Thierry Frebourg, David E. Goldgar, Christopher D. Heinen, Elke Holinski-Feder, Maija Kohonen-Corish, Kristina Lagerstedt Robinson, Suet Yi Leung, Alexandra Martins, Pal Moller, Monika Morak, Minna Nystrom, Paivi Peltomaki, Marta Pineda, Ming Qi, Rajkumar Ramesar, Lene Juel Rasmussen, Brigitte Royer-Pokora, Rodney J. Scott, Rolf Sijmons, Sean V. Tavtigian, Carli M. Tops, Thomas Weber, Juul Wijnen, Michael O. Woods, on behalf of InSiGHT, Finlay Macrae, Maurizio Genuardi

Background This study investigated variation in NR1I2 and NR1I3 and its effect on plasma efavirenz levels in HIV/AIDS patients. Variability in plasma drug levels has largely led research on identifying causative variants in drug metabolising enzyme (DME) genes, with little focus on the nuclear receptor genes NR1I2 and NR1I3 , coding for PXR and CAR, respectively, that are involved in regulating DMEs. Methods 464 Bantu-speaking South Africans comprising of HIV/AIDS patients on efavirenz-based treatment (n=301) and 163 healthy subjects were genotyped for 6 SNPs in NR1I2 and NR1I3 . 32 of the 301 patients had their DNA binding domains (DBDs) in NR1I2 and NR1I3 sequenced. Results Significantly decreased efavirenz plasma concentrations were observed in patients carrying the NR1I3 rs3003596C/C and T/C genotypes (P=0.015 and P=0.010, respectively). Sequencing resulted in the discovery of a further 13 SNPs, 3 of which are novel variants in the DBD of NR1I2 . There were significant differences in the distribution of NR1I2 and NR1I3 SNPs between South Africans when compared to Caucasian, Asian and Yoruba population groups. Conclusion For the realisation of personalised medicine, PXR and CAR genetic variation should be taken into consideration because of their involvement in the regulation of DMEs.

Purpose: Based on the previous indications of founder ATP-binding cassette sub-family A member 4 gene (ABCA4) mutations in a South African subpopulation, the purpose was to devise a mechanism for identifying common disease-causing mutations in subjects with ABCA4-associated retinopathies (AARs). Facilitating patient access to this data and determining the frequencies of the mutations in the South African population would enhance the current molecular diagnostic service offered.Methods: The majority of subjects in this study were of Caucasian ancestry and affected with Stargardt macular dystrophy. The initial cohort consisted of DNA samples from 181 patients, and was screened using the ABCR400 chip. An assay was then designed to screen a secondary cohort of 72 patients for seven of the most commonly occurring ABCA4 mutations in this population. A total of 269 control individuals were also screened for the seven ABCA4 mutations.Results: Microarray screening results from a cohort of 181 patients affected with AARs revealed that seven ABCA4 mutations (p.Arg152*, c.768G>T, p.Arg602Trp, p.Gly863Ala, p.Cys1490Tyr, c.5461-10T>C, and p.Leu2027Phe) occurred at a relatively high frequency. The newly designed genetic assay identified two of the seven disease-associated mutations in 28/72 patients in a secondary patient cohort. In the control cohort, 12/269 individuals were found to be heterozygotes, resulting in an estimated background frequency of these mutations in this particular population of 4.46 per 100 individuals.Conclusions: The relatively high detection rate of seven ABCA4 mutations in the primary patient cohort led to the design and subsequent utility of a multiplex assay. This assay can be used as a viable screening tool and to reduce costs and laboratory time. The estimated background frequency of the seven ABCA4 mutations, together with the improved diagnostic service, could be used by counselors to facilitate clinical and genetic management of South African families with AARs.