Genes in the aetiology of oculocutaneous albinism in Sub-Saharan Africa and a possible role in tuberculosis susceptibility

ABSTRACT In southern Africa, oculocutaneous albinism (OCA) is the most common autosomal recessive disease amongst black Africans, occurring with a prevalence of approximately 1 in 3 900 individuals. OCA occurs in southern African Caucasoids with a frequency that reflects the European origins of this population, approximately 1 in 20-30 000. OCA type 1 is caused by mutations in the tyrosinase gene on chromosome 11q. Tyrosinase mutations occur in the Caucasoid population but are extremely rare in black Africans. OCA type 2 is caused by mutations in the P gene on chromosome 15q. P gene mutations occur in both the black and Caucasoid populations. A sub-type of OCA2 seen in black individuals, brown OCA (BOCA), is also caused by mutations at the P gene locus. A mutation screen was undertaken to identify disease-causing mutations in a group of OCA subjects from Sub-Saharan Africa. A common P gene mutation had been identified in the black population, a 2.7 kb intragenic deletion, accounting for 78% of P gene mutations in this group. No common tyrosinase mutations have been identified to date, in any population. A cohort of OCA subjects from South Africa, Lesotho, Zambia and the Central African Republic (CAR) were available for study in our laboratory. All subjects were screened for the 2.7 kb deletion mutation. Subjects homozygous for this mutation were excluded from further study. Subjects where one or two mutations remained to be identified were included in a mutation screen (63 blacks and 9 Caucasoids). Depending on the clinical categorisation of the type of albinism, subjects were screened for P gene mutations only (black OCA2) or were screened for P gene mutations and tyrosinase mutations (BOCA, unclassified black OCA and unclassified Caucasoid OCA). All 72 subjects were screened for P gene mutations and ten putative pathogenic mutations were identified. In the group of black OCA2 patients, four mutations which are likely to be pathogenic were found: A334V, 614delA, 683insT and 727insG. Mutations were identified in four individuals with an unusual hypopigmentation phenotype: E678K was found in the homozygous state in an individual from the CAR. A second individual was found to be a compound heterozygote for the I370T and the L688F mutations. A third individual was found to be heterozygous for the I370T mutation. Three P gene mutations were found in the Caucasoid sample: IVS 14-2 (a→g), V350M and P743L. No further mutations were identified in the BOCA sample. The P gene screen comprised 72 subjects, but 40 were heterozygous for the 2.7 kb deletion, therefore (144 minus 40 alleles) 104 alleles remained to be identified. Identification of 12/104 alleles means that a further 11.5% of the unknown P gene mutations are now accounted for. Thirty three of the 72 subjects were included in a further mutation screen – at the tyrosinase locus. Four mutations were identified, all in the Caucasoid group. Compound heterozygosity was shown in two individuals, one carrying the mutations, E294K and A490D and the other, P431T and T373K. Following mutation analysis of the P gene, it was apparent that a proportion of mutations did not lie in the coding region of the gene and it was proposed that some of the remaning unidentified mutations might be found in the 5’control or promoter region of the gene. At that time, sequence data for the region upstream of the P gene was not known, and so an attempt was made to clone the 5’region of the P gene. Two approaches were adopted – a bacterial artificial chromosome (BAC) known to contain this region was subcloned; and secondly, an inverse PCR experiment was undertaken. Neither experiment was successful in generating P gene promoter sequence. Variation at the P locus was investigated in a second context. This region of chromosome 15q was implicated as a host susceptibility locus for the infectious disease, tuberculosis (TB). A case-control study was undertaken to compare the frequencies of five intragenic, polymorphic markers in the P gene: the 2.7 kb deletion, the R305W polymorphism and the microsatellite markers, D15S1533, D15S1536 and D15S1537, between a group of black South African TB patients from Gauteng and healthy community controls and between a group of mixed-ancestry (Coloured) TB patients and healthy controls from the Western Cape region. Presence or absence of the 2.7 kb deletion mutation does not appear to influence susceptibility to TB in either the black or Coloured population samples studied here. The W allele of the R305W polymorphism is significantly (p<0.05) more common in the black patient group than in the black control group, suggesting it may be in linkage disequilibrium with a disease susceptibility allele. Microsatellite marker analysis showed that, in the black population, allele 18 at the D15S1533 locus is significantly (p<0.05) associated with susceptibility to TB. In the Cape Coloured population, alleles 20 and 27 at the D15S1533 locus, allele 12 at the D15S1536 locus and allele 16 at the D15S1537 locus are over represented in the patient group suggesting they may be markers for increased susceptibility to TB. Further, in the Coloured population alleles 12, 13 and 15 at the D15S1537 locus showed significant (p<0.05) association with normal controls and may be in linkage disequilibrium with protective or resistance alleles. The results of this study support the proposal of a TB susceptibility locus on chromosome 15q. OCA-causing mutations have been identified, but many remain elusive. Further characterisation of this region will give us a better understanding of the biological consequences of variation both within and around the P locus

Long-term cost implications for cochlear implant recipients

Thesis (MAud)--University of Stellenbosch, 2011.ENGLISH ABSTRACT: Cochlear implantation is an expensive but cost-effective intervention which must be used for life. It can provide individuals with severe-to-profound hearing loss improved sound perception in comparison to that obtained using hearing aids. In South Africa implants are not state subsidised, and related costs need to be covered by implant recipients. Cochlear implant teams thus need to ensure that individuals, who are selected, will benefit from the device and will be able to use it for their lifetime. Implantees should know the immediate and potential future costs involved, to be able to decide on its affordability. The primary aim of this study was to determine the immediate and long-term costs of cochlear implantation. One hundred and fifty four implant recipients from the Tygerberg Hospital- University of Stellenbosch Cochlear Implant Unit in Cape Town, South Africa were surveyed. Costs were categorized according to the time period post implantation and were converted to Constant Rands (June 2010) using the Consumer Price Index to allow for comparison in real terms over time. In the first 10 years of implantation the average estimated costs incurred by adult implantees totalled R379 626, and children R455 225. The findings showed that the initial purchase of the implant system was the most substantial cost involved (currently R221 000). Upgrading the speech processor, which on the average took place every 7 years, was the second highest cost subjects encountered (currently R85 000). The cost of spares (on average R276 per year) and repairs (R3000 per repair) increased with duration of use. Battery costs ranged between R1200 and R3372 per year and insurance costs averaged R4040 per year. Most appointments took place in the first two years following implantation. Average travel costs during the first two years were R1024 for those within 50km of the implant unit and R8645 for those living more than 1000km away. Accommodation costs for non-local recipients, peaked during this period (on average R3390). Additional rehabilitation services for paediatric implantees cost an estimated R37 159 in the first five years after implantation. Subjects advised potential implantees to save, budget and plan for the high costs involved in implantation, as well as to join a medical aid which could assist with the costs involved. The findings of the study hold great relevance for both implantees and cochlear implant professionals. Careful consideration of the financial implications of cochlear implantation is critically important in the South African context to ensure that recipients are successful longterm cochlear implant users. Although the actual costs in the study were related to the one implant system used at Tygerberg Hospital-University of Stellenbosch Cochlear Implant Unit, it is believed that the types and amounts of costs involved hold relevance for all individuals implanted in South Africa.AFRIKAANSE OPSOMMING: Kogleêre inplantering is ‘n duur maar koste-effektiewe prosedure wat lewenslank gebruik moet word. Dit verskaf aan individue met erge-tot-uitermatige gehoorverlies verbeterde klankpersepsie in vergelyking met dié wat gehoorapparate gebruik. In Suid Afrika word kogleêre inplantings nie deur die staat gesubsidieer nie en koste moet deur die inplantgebruiker verhaal word. Kogleêre inplantingspanne moet gevolglik verseker dat individue wat geselekteer word daarby baat sal vind en lewenslank sal kan gebruik. Inplantgebruikers moet bewus wees van die onmiddelike, sowel as langtermyn onkoste. Die primêre doel van hierdie studie was om die onmiddelike en langtermyn onkoste van implanterings te bepaal. Een honderd vier en vyftig inplantgebruikers van die Tygerberg Hospitaal-Universiteit Stellenbosch Kogleêre Inplantingseenheid in Kaapstad, Suid Afrika is gebruik vir die studie. Onkoste was gekatogoriseer ten opsigte van die periode van tyd postinplantering en dit is omgeskakel na konstante Randwaarde (Junie 2010) deur die Gebruikers Prys Indeks te gebruik sodat vergelykings gemaak kon word in reële terme oor tyd. Gedurende die eerste 10 jaar na inplantering was die geskatte onkoste by volwasse inplantgebruikers R379 626 en by die pediatriese groep was dit R455 225. Bevindings het aangedui dat die aanvanklike aankoop van die inplantsisteem die grootste onkoste behels het (huidig R221 000). Opgradering van die prosesseerder, gemiddeld elke 7 jaar, was die tweede hoogste onkoste, naamlik R85 000. Die gemiddelde koste van spaaronderdele was R276 per jaar. Herstelkoste het R3000 per herstelling beloop. Koste van spaaronderdele en herstelkoste het met duur van gebruik vermeerder. Batteryonkoste het gewissel tussen R1200 en R3372 per jaar. Onkoste van jaarlikse versekering was gemiddeld R4040. Meeste afsprake het gedurende die eerste twee jaar plaasgevind. Vervoeronkoste gedurende hierdie periode was R1024 vir die wat binne 50km woon en R8645 vir dié meer as ‘n 1000km ver. Akkommodasie koste het ‘n piek gedurende hierdie periode bereik (gemiddeld R3390). Addisionele rehabilitasie dienste vir pediatriese inplantgebruikers was gemiddeld R37159 gedurende die eerste vyf jaar. Die proefpersone het aanbeveel dat potensiële inplantgebruikers moet spaar, begroot en beplan vir die hoë onkoste en is aanbeveel om aan te sluit by ‘n mediese fonds. Die bevindinge van die studie is van belang vir beide ontvangers sowel as inplantingspanne. Bewusmaking van die finansiële implikasies van kogleêre inplantering is van kritiese belang om suksesvolle langtermyn gebruik te verseker. Alhoewel die werklike onkoste in die studie van toepassing is op een inplanting sisteem wat by Tygerberg Hospitaal-Universiteit Stellenbosch Kogleêre Inplantingseenheid gebruik word, kan dit aangeneem word dat die tipes en hoeveelheid onkoste van toepassing is op alle individue in Suid Afrika wat kogleêre inplantings ontvang

Net Reclassification Indices for Evaluating Risk Prediction Instruments: A Critical Review

Background Net Reclassification Indices (NRI) have recently become popular statistics for measuring the prediction increment of new biomarkers. Methods In this review, we examine the various types of NRI statistics and their correct interpretations. We evaluate the advantages and disadvantages of the NRI approach. For pre-defined risk categories, we relate NRI to existing measures of the prediction increment. We also consider statistical methodology for constructing confidence intervals for NRI statistics and evaluate the merits of NRI-based hypothesis testing. Conclusions Investigators using NRI statistics should report them separately for events (cases) and nonevents (controls). When there are two risk categories, the NRI components are the same as the changes in the true and false positive rates. We advocate use of true and false positive rates and suggest it is more useful for investigators to retain the existing, descriptive terms. When there are three or more risk categories, we recommend against NRI statistics because they do not adequately account for clinically important differences in movements among risk categories. The category-free NRI is a new descriptive device designed to avoid pre-defined risk categories. The category-free NRI suffers from many of the same problems as other measures such as the area under the receiver operating characteristic curve. In addition, the category-free NRI can mislead investigators by overstating the incremental value of a biomarker, even in independent validation data. When investigators want to test a null hypothesis of no prediction increment, the well-established tests for coefficients in the regression model are superior to the NRI. If investigators want to use NRI measures, their confidence intervals should be calculated using bootstrap methods rather than published variance formulas. The preferred single-number summary of the prediction increment is the improvement in the Net Benefit

Biology and genetics of oculocutaneous albinism and vitiligo – common pigmentation disorders in southern Africa

Pigmentation disorders span the genetic spectrum from single-gene autosomal recessive disorders such as oculocutaneous albinism (OCA), the autosomal dominant disorder piebaldism to X-linked ocular albinism and multifactorial vitiligo. OCA connotes a group of disorders that result in hypopigmented skin due to decreased melanin production in melanocytes and loss of visual acuity. There are four non-syndromic forms, OCA1-4, which are classified based on the gene that is mutated (tyrosinase, OCA2, tyrosinase-related protein 1 and SLC45A2, respectively). Despite the fact that multiple genes account for the various forms of OCA, the phenotypes of all four forms result from disruption in the maturation and trafficking of the enzyme tyrosinase. OCA2 is the most prevalent autosomal recessive disorder among southern African blacks, affecting 1/3 900 individuals; while OCA3, although rare, is most prevalent in southern Africa. Another common pigmentation disorder in southern Africa is vitiligo, which affects 1 - 2% of people worldwide. Vitiligo is a complex, acquired disorder in which melanocytes are destroyed due to an autoimmune response. The aetiology underlying this disorder is poorly understood, although recent genetic association studies have begun to shed light on the contributing factors. Pigmentation disorders have significant psychosocial implications and co-morbidities, yet therapies are still lacking. Recent progress in our understanding of the pathobiology of both albinism and vitiligo may herald novel treatment strategies for these disorders.

The Vehicle, Fall 1988

Table of Contents Cover LetterBob Zordanipage 3 Letter to Harrington StreetBob Zordanipage 4 The Only TruthBob Zordanipage 5 They\u27d Gone to a MovieMatt Mansfieldpage 6 The LocketMonica Grothpage 6 The Sleep of BabesMonica Grothpage 7 Techni-Color Characters in a Black and White TownMonica Grothpage 8 The HorseRodger Patiencepage 9 ValaciaRobyn Kerrpage 10 Gatsby\u27s LightJim Reedpage 11 Millions of MeJim Reedpage 12 View from the StreetsSteven M. Beamerpage 13 When Headlights on the HighwayMichael Salempage 23 Concrete AffairsMichael Salempage 24 The Middle of the StreetMichael Salempage 25 Scent of a StormMichael Salempage 26 The FishermanAngie Geraldpage 27 OrgansPatrick Peterspage 33 CarpentryPatrick Peterspage 34 FishingPatrick Peterspage 35 Autumn Poem for a Friend In a Printing PlantPatrick Peterspage 36https://thekeep.eiu.edu/vehicle/1051/thumbnail.jp

The Vehicle, Fall 1988

Table of Contents Cover LetterBob Zordanipage 3 Letter to Harrington StreetBob Zordanipage 4 The Only TruthBob Zordanipage 5 They\u27d Gone to a MovieMatt Mansfieldpage 6 The LocketMonica Grothpage 6 The Sleep of BabesMonica Grothpage 7 Techni-Color Characters in a Black and White TownMonica Grothpage 8 The HorseRodger Patiencepage 9 ValaciaRobyn Kerrpage 10 Gatsby\u27s LightJim Reedpage 11 Millions of MeJim Reedpage 12 View from the StreetsSteven M. Beamerpage 13 When Headlights on the HighwayMichael Salempage 23 Concrete AffairsMichael Salempage 24 The Middle of the StreetMichael Salempage 25 Scent of a StormMichael Salempage 26 The FishermanAngie Geraldpage 27 OrgansPatrick Peterspage 33 CarpentryPatrick Peterspage 34 FishingPatrick Peterspage 35 Autumn Poem for a Friend In a Printing PlantPatrick Peterspage 36https://thekeep.eiu.edu/vehicle/1051/thumbnail.jp

The Integrity and Yield of Genomic DNA Isolated from Whole Blood Following Long-Term Storage at -30°C.

Long-term storage of whole blood can affect the integrity of DNA if it is not done under optimal conditions. The aim of this study was to determine whether long-term storage (2-19 years) of whole blood samples at -30°C had a negative effect on the quality or quantity of genomic DNA that could be recovered at extraction. Genomic DNA was isolated from 2758 whole blood samples collected in 4 mL EDTA vacutainers from 1997 to 2012. DNA was extracted using the Qiagen® FlexiGene® DNA kit. The average storage duration at -30°C was 12 years. The quality and quantity of the isolated DNA were assessed using spectrophotometry (NanoDrop™), a fluorometric assay for double-stranded DNA (Qubit™), and agarose gel electrophoresis. The mean DNA yield per sample was found to be 114 μg from whole blood volumes that ranged from 0.5 to 4 mL. The mean A260/280 ratio and median A260/280 ratios were both 1.8. No correlation was found between the duration of storage and the total yield or the quality of DNA extracted. These data suggest that high-quality DNA can be extracted from whole blood samples that are stored at -30°C for up to 19 years