Molecular Analysis of a Case of Thanatophoric Dysplasia Reveals Two de novo FGFR3 Missense Mutations located in cis

Objectives: Thanatophoric dysplasia (TD) is the most common form of lethal skeletal dysplasia. It is primarily an autosomal dominant disorder and is characterised by macrocephaly, a narrow thorax, short ribs, brachydactyly, and hypotonia. In addition to these core phenotypic features, TD type I involves micromelia with bowed femurs, while TD type II is characterised by micromelia with straight femurs and a moderate to severe clover-leaf deformity of the skull. Mutations in the FGFR3 gene are responsible for all cases of TD reported to date. The objective of the study here was to delineate further the mutational spectrum responsible for TD. Methods: Conventional polymerase chain reaction (PCR), allele-specific PCR, and sequence analysis were used to identify FGFR3 gene mutations in a fetus with a lethal skeletal dysplasia consistent with TD, which was detected during a routine antenatal ultrasound examination. Results: In this report we describe the identification of two de novo missense mutations in cis in the FGFR3 gene (p.Asn540Lys and p.Val555Met) in a fetus displaying phenotypic features consistent with TD. Conclusion: This is the second description of a case of TD occurring as a result of double missense FGFR3 gene mutations, suggesting that the spectrum of mutations involved in the pathogenesis of TD may be broader than previously recognised

Life of the Woods: A Study of Emily Dickinson

Beginning with T.W. Higginson, the poet’s first public critic and posthumous editor, the prevailing view of Emily Dickinson has been of a maker of “wonderful strokes and felicities, and yet an incomplete and unsatisfactory whole,” a view that is often based on her perceived strangeness as a person. More recently, Virginia Jackson has advanced the view of Dickinson’s poetry as being poorly served by modern methods of practical criticism, “dependent on their artifactual contexts” and on thoughts “too intimate for print.” Unabashedly practical in its approach, this thesis argues that the general shape of Dickinson’s life reveals her writings as the product of her personal quest for growth, and that, further, her reclusive habits reflect this quest. Dickinson’s removal from the ordinary modes of life in her town parallels Henry David Thoreau’s more transient life in the woods. No less than Thoreau, Dickinson wished “to live deliberately, to front only the essential facts of life,” but the combined pressures of gender and social situation placed restrictions on how Dickinson might do so as a woman. Yet while she did not take up an abode in the woods, Dickinson’s home life enabled her to live in the manner of the woods—a symbol of inexhaustible diversity in the poet’s imagination, and an endless source of significance beyond her conscious will. The title of the study hints at the mode of life the poet associates with this uncharted, enchanted place. The Introduction uses Dickinson’s early letters to Higginson to trace out her project as a poet in light of mid-nineteenth century critical principles. It shows how the poet repeatedly draws a distinction between herself as a person and herself as a poet, and how the theory of organic form which was dominant in her time helps to clarify her aesthetic achievements, while it also offers an explanation of why she never sought to publish her works. The main argument of this thesis is composed of two parts. Part I is composed of three chapters, all of which concern challenges posed by Dickinson’s writing. The first chapter considers several significant aspects of Dickinson’s autograph manuscripts, rejecting the materialist theories of some recent writers on the subject while also considering what the manuscripts tell us about the poet on the page. The second and third chapters explore the main purpose of Dickinson’s non-verbal notation, her use of non-standard conventions of orthography and punctuation (including capitalisation), and also her use of line breaks. Part II is also composed of three chapters, each of which focuses on distinct topics to offer new perspectives on Dickinson’s poems. The fourth chapter examines several poems in light of the tradition of natural visionary wisdom that flourished in New England in Dickinson’s time. The fifth chapter applies the literary conception of paradox to several of Dickinson’s more challenging poems, showing how the mode of paradox allows her to grasp the fuller sense of experience. The subject of the last chapter is death, immortality, and the “Immortality” the poet associates with enchanted earthly experience. The Conclusion describes an important function of Dickinson’s poetry—it offers to make us conscious of what is strange, wonderful, and unknowable in the world. A few prospects for the next stage of the study are also described

Determination of Pathogenicity of Breast Cancer 1 Gene Variants using the American College of Medical Genetics and Genomics and the Association for Molecular Pathology Guidelines

Objectives: Molecular diagnostic laboratories screen for mutations in disease-causing genes in order to confirm a clinical diagnosis. The classification of DNA variants as ‘pathogenic’ or ‘likely pathogenic’ mutations creates a workflow bottleneck, which becomes increasingly challenging as greater number of genes are screened. The classification challenge is also acute if there are conflicting reports regarding pathogenicity and differing classification criteria between laboratories. This study aimed to compare two procedures for the classification of variants in the breast cancer (BRCA)1 gene. Methods: This bioinformatic study was conducted at LabPLUS, Auckland, New Zealand, from February to June 2017. DNA was extracted from peripheral blood samples of 30 patients and gene library construction was carried out using a commercially available targeted panel for the BRCA1 and BRCA2 genes. The genes were subsequently sequenced and the sequence data analysed. The guidelines published by the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/ AMP) provides a comprehensive framework for the interpretation of variants in genes that are associated with Mendelian disorders. The use of these guidelines were compared to the variant classifications that were achieved by reference to those reported in the BRCA Exchange database. Results: The results showed concordance between the two classification protocols for a panel of 30 BRCA1 gene variants, although the transparency in following the ACMG/AMP guidelines provides a diagnostic laboratory with a generalisable approach that allows laboratorydirected revisions to be undertaken in light of new information. Conclusion: The ACMG/AMP-based guidelines were applied to a cohort of patients with BRCA1 gene variants. The use of these guidelines provides a system which creates consistency in variant interpretation and supports subsequent clinical management.Keywords: BRCA1 Gene; Bioinformatics; DNA Sequencing; Nonsense Codon; Splice Donor Site; New Zealand

The effect of the Madden-Julian Oscillation on station rainfall and river level in the Fly River system, Papua New Guinea

The Madden-Julian oscillation (MJO) is the dominant mode of intraseasonal variability in tropical rainfall on the large scale, but its signal is often obscured in individual station data, where effects are most directly felt at the local level. The Fly River system, Papua New Guinea, is one of the wettest regions on Earth and is at the heart of the MJO envelope. A 16 year time series of daily precipitation at 15 stations along the river system exhibits strong MJO modulation in rainfall. At each station, the difference in rainfall rate between active and suppressed MJO conditions is typically 40% of the station mean. The spread of rainfall between individual MJO events was small enough such that the rainfall distributions between wet and dry phases of the MJO were clearly separated at the catchment level. This implies that successful prediction of the large-scale MJO envelope will have a practical use for forecasting local rainfall. In the steep topography of the New Guinea Highlands, the mean and MJO signal in station precipitation is twice that in the satellite Tropical Rainfall Measuring Mission 3B42HQ product, emphasizing the need for ground-truthing satellite-based precipitation measurements. A clear MJO signal is also present in the river level, which peaks simultaneously with MJO precipitation input in its upper reaches but lags the precipitation by approximately 18 days on the flood plains

Array-based Identification of Copy Number Changes in a Diagnostic Setting : Simultaneous gene-focused and low resolution whole human genome analysis

Objectives: The aim of this study was to develop and validate a comparative genomic hybridisation (CGH) array that would allow simultaneous targeted analysis of a panel of disease genes and low resolution whole genome analysis. Methods: A bespoke Roche NimbleGen 12x135K CGH array (Roche NimbleGen Inc., Madison, Wisconsin, USA) was designed to interrogate the coding regions of 66 genes of interest, with additional widelyspaced backbone probes providing coverage across the whole genome. We analysed genomic deoxyribonucleic acid (DNA) from 20 patients with a range of previously characterised copy number changes and from 8 patients who had not previously undergone any form of dosage analysis. Results: The custom-designed Roche NimbleGen CGH array was able to detect known copy number changes in all 20 patients. A molecular diagnosis was also made for one of the additional 4 patients with a clinical diagnosis that had not been confirmed by sequence analysis, and carrier testing for familial copy number variants was successfully completed for the remaining four patients. Conclusion: The custom-designed CGH array described here is ideally suited for use in a small diagnostic laboratory. The method is robust, accurate, and cost-effective, and offers an ideal alternative to more conventional targeted assays such as multiplex ligation-dependent probe amplification

Implications of a Chr7q21.11 Microdeletion and the Role of the PCLO Gene in Developmental Delay

We report here a 4-year-old boy with global developmental delay who was referred for karyotyping and fragile X studies. A small interstitial deletion on chromosome 7 at band 7q21 was detected in all cells examined. Subsequent molecular karyotype analysis gave the more detailed result of a 6.3 Mb heterozygous deletion involving the interstitial chromosome region 7q21.11. In this relatively gene-poor region, the presynaptic cytomatrix protein, Piccolo (PCLO) gene appears to be the most likely candidate for copy number loss leading to a clinical phenotype. G-banded chromosome analysis of the parents showed this deletion was inherited from the father. Molecular karyotype analysis of the father’s genome confirmed that it was the same deletion as that seen in the son; however, the father did not share the severity of his son’s phenotype. This cytogenetically-visible deletion may represent another example of a chromosomal rearrangement conferring a variable phenotype on different family members