Mutation screening of retinal dystrophy patients by targeted capture from tagged pooled DNAs and next generation sequencing.

Purpose: Retinal dystrophies are genetically heterogeneous, resulting from mutations in over 200 genes. Prior to the development of massively parallel sequencing, comprehensive genetic screening was unobtainable for most patients. Identifying the causative genetic mutation facilitates genetic counselling, carrier testing and prenatal/pre-implantation diagnosis, and often leads to a clearer prognosis. In addition, in a proportion of cases, when the mutation is known treatment can be optimised and patients are eligible for enrolment into clinical trials for gene-specific therapies. Methods: Patient genomic DNA was sheared, tagged and pooled in batches of four samples, prior to targeted capture and next generation sequencing. The enrichment reagent was designed against genes listed on the RetNet database (July 2010). Sequence data were aligned to the human genome and variants were filtered to identify potential pathogenic mutations. These were confirmed by Sanger sequencing. Results: Molecular analysis of 20 DNAs from retinal dystrophy patients identified likely pathogenic mutations in 12 cases, many of them known and/or confirmed by segregation. These included previously described mutations in ABCA4 (c.6088C>T,p.R2030*; c.5882G>A,p.G1961E), BBS2 (c.1895G>C,p.R632P), GUCY2D (c.2512C>T,p.R838C), PROM1 (c.1117C>T,p.R373C), RDH12 (c.601T>C,p.C201R; c.506G>A,p.R169Q), RPGRIP1 (c.3565C>T,p.R1189*) and SPATA7 (c.253C>T,p.R85*) and new mutations in ABCA4 (c.3328+1G>C), CRB1 (c.2832_2842+23del), RP2 (c.884-1G>T) and USH2A (c.12874A>G,p.N4292D). Conclusions: Tagging and pooling DNA prior to targeted capture of known retinal dystrophy genes identified mutations in 60% of cases. This relatively high success rate may reflect enrichment for consanguineous cases in the local Yorkshire population, and the use of multiplex families. Nevertheless this is a promising high throughput approach to retinal dystrophy diagnostics

Wetland Manipulation in the Yalahau Region of the Northern Maya Lowlands

Manipulation of wetlands for agricultural purposes by the ancient Maya of southern Mexico and Central America has been a subject of much research and debate since the 1970s. Evidence for wetland cultivation systems, in the form of drained or channelized fields, and raised planting platforms, has been restricted primarily to the southern Maya Lowlands. New research in the Yalahau region of Quintana Roo, Mexico, has recorded evidence for wetland manipulation in the far northern lowlands, in the form of rock alignments that apparently functioned to control water movement and soil accumulation in seasonally inundated areas. Nearby ancient settlements date primarily to the Late Preclassic period (ca. 100 B.C. to A.C. 350), and this age is tentatively attributed to wetland management in the area

Landuse and soil degradation in the southern Maya lowlands, from Pre-Classic to Post-Classic times : The case of La Joyanca (Petén, Guatemala)

International audienceThis work focuses on the impact of Maya agriculture on soil degradation. In site and out site studies in the area of the city of La Joyanca (NW Petén) show that "Maya clays" do not constitute a homogeneous unit, but represent a complex sedimentary record. A high resolution analysis leads us to document changes in rates and practices evolving in time in relation with major socio-political and economic changes. It is possible to highlight extensive agricultural practices between Early Pre-classical to Late Pre-classical times. Intensification occurs in relation with reduction of the fallow duration during Pre-classic to Classic periods. The consequences of these changes on soil erosion are discussed. However, it does not seem that the agronomic potential of the soils was significantly degraded before the end of the Classic period

Identification of a novel pathogenic OTOF variant causative of nonsyndromic hearing loss with high frequency in the Ashkenazi Jewish population

Anastasia M Fedick,1 Chaim Jalas,2 Ananya Swaroop,1 Eric E Smouha,3 Bryn D Webb1 1Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; 2Bonei Olam, Center for Rare Jewish Genetic Disorders, Brooklyn, NY, USA; 3Department of Otolaryngology, Icahn School of Medicine at Mount Sinai, New York, NY, USA Abstract: Mutations in the OTOF gene have previously been shown to cause nonsyndromic prelingual deafness (DFNB9, OMIM 601071) as well as auditory neuropathy/dys-synchrony. In this study, the OTOF NM_194248.2 c.5332G>T, p.Val1778Phe variant was identified in a large Ashkenazi Jewish family as the causative variant in four siblings with hearing loss. Our analysis reveals a carrier frequency of the OTOF c.5332G>T, p.Val1778Phe variant of 1.27% in the Ashkenazi Jewish population, suggesting that this variant may be a significant contributor to nonsyndromic sensorineural hearing loss and should be considered for inclusion in targeted hearing loss panels for this population. Of note, the degree of hearing loss associated with this phenotype ranged from mild to moderately severe, with two of the four siblings not known to have hearing loss until they were genotyped and underwent pure tone audiometry and auditory brainstem response testing. The phenotypic variability along with the auditory neuropathy/dys-synchrony, which allows for the production of otoacoustic emissions, supports that nonsyndromic hearing loss caused by OTOF mutations may be much more common in the Ashkenazi Jewish population than currently appreciated due to a lack of diagnosis. Keywords: hearing loss, OTOF, c.5332G>T, p.Val1778Phe, Ashkenazi Jewish, otoferlin&nbsp