dbDNV: a resource of duplicated gene nucleotide variants in human genome

Gene duplications are scattered widely throughout the human genome. A single-base difference located in nearly identical duplicated segments may be misjudged as a single nucleotide polymorphism (SNP) from individuals. This imperfection is undistinguishable in current genotyping methods. As the next-generation sequencing technologies become more popular for sequence-based association studies, numerous ambiguous SNPs are rapidly accumulated. Thus, analyzing duplication variations in the reference genome to assist in preventing false positive SNPs is imperative. We have identified >10% of human genes associated with duplicated gene loci (DGL). Through meticulous sequence alignments of DGL, we systematically designated 1 236 956 variations as duplicated gene nucleotide variants (DNVs). The DNV database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) has been established to promote more accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL and DNV searches, respectively. In addition, the dbDNV contains 304 110 DNV-coupled SNPs. From DNV-coupled SNP search, users observe which SNP records are also variants among duplicates. This is useful while ∼58% of exonic SNPs in DGL are DNV-coupled. Because of high accumulation of ambiguous SNPs, we suggest that annotating SNPs with DNVs possibilities should improve association studies of these variants with human diseases

Depth-dependent target strengths of gadoids by the boundary-element method

Author Posting. © Acoustical Society of America, 2003. This article is posted here by permission of Acoustical Society of America for personal use, not for redistribution. The definitive version was published in Journal of the Acoustical Society of America 114 (2003): 3136-3146, doi:10.1121/1.1619982.The depth dependence of fish target strength has mostly eluded experimental investigation because of the need to distinguish it from depth-dependent behavioral effects, which may change the orientation distribution. The boundary-element method (BEM) offers an avenue of approach. Based on detailed morphometric data on 15 gadoid swimbladders, the BEM has been exercised to determine how the orientation dependence of target strength changes with pressure under the assumption that the fish swimbladder remains constant in shape and volume. The backscattering cross section has been computed at a nominal frequency of 38 kHz as a function of orientation for each of three pressures: 1, 11, and 51 atm. Increased variability in target strength and more abundant and stronger resonances are both observed with increasing depth. The respective backscattering cross sections have been averaged with respect to each of four normal distributions of tilt angle, and the corresponding target strengths have been regressed on the logarithm of fish length. The tilt-angle-averaged backscattering cross sections at the highest pressure have also been averaged with respect to frequency over a 2-kHz band for representative conditions of insonification. For all averaging methods, the mean target strength changes only slightly with depth.This work began with sponsorship by the European Commission through its RTD-program, Contract No. MAS3-CT95-0031 (BASS), and was completed with support by the Office of Naval Research, Contract No. N000140310368

Content and Quality of Motor Initiatives in the Support of People With Profound Intellectual and Multiple Disabilities

Motor activation is rarely integrated into the support of people with profound intellectual and multiple disabilities (PIMD), which might be the result of the limited evidence‐based knowledge in this field. Practitioners have recently been developing several motor initiatives for people with PIMD, but it remains unclear about what core elements the motor initiatives actually consist of and to what level of quality it is implemented in practice. This study aims to offer an overview and analysis of the content and quality of motor initiatives actually in use for people with PIMD. Motor initiatives were explored by asking practitioners to complete an online inventory form. Documents, expert knowledge, and observations were used to collect data about the characteristics of the motor initiatives. The quality of the motor initiatives which met our eligibility criteria, was analyzed on the basis of the level of evidence for their effectiveness. The inventory yielded 118 motor initiatives of which 17 met the eligibility criteria. We identified four motor initiatives reflecting an approach to motorically activate people with PIMD within various activities, three including power‐assisted exercises, three with aquatic exercises, two frameworks which integrated motor activities into their daily programs, two methods which included small‐scale activities, two rhythmic movement therapies, and one program including gross motor activities. We found limited indications for descriptive evidence from 17 initiatives, limited or no indications for theoretical evidence from 12 and five initiatives respectively, and none of the initiatives provided a causal level of evidence for effectiveness. A wide variety of motor initiatives is used in current practice to activate persons with PIMD, although their effectiveness is actually unproven. Science and practice should cooperate to develop an evidence‐based understanding to ensure more evidence‐based support for the motor activation of people with PIMD in the future

Cancer risks by gene, age, and gender in 6350 carriers of pathogenic mismatch repair variants: findings from the Prospective Lynch Syndrome Database

Lynch syndrome (LS) results from pathogenic variants in the mismatch repair (MMR) genes and is the most common hereditary cancer syndrome, affecting an estimated 1 in 300 individuals. Pathogenic variants in each of the MMR genes path_MLH1, path_MSH2, path_MSH6, and path_PMS2 result in different risks for cancers in organs including the colorectum, endometrium, ovaries, stomach, small bowel, bile duct, pancreas, and upper urinary tract. Accurate estimates of these risks are essential for planning appropriate approaches to the prevention or early diagnosis of cancers but the robustness of previous studies has been limited by factors including retrospective design,1,2 lack of validation in independent cohorts,3-5 and inconsistent classification of genetic variants. Unexpected findings from previous studies have included path_MLH1 and path_MSH2 carriers appearing to have a lifetime risk of colorectal cancer (CRC) of approximately 50%, despite surveillance colonoscopy,6-8 and that shorter intervals between colonoscopies do not seem to reduce the incidence of CRC in LS.9,10 These findings challenge the assumptions that CRC in LS usually develops from a noninfiltrative adenoma precursor and that CRC can be prevented by colonoscopic detection and removal of adenomas in the colon and rectum. Additionally, previous studies in the Prospective Lynch Syndrome Database (PLSD) have shown no increase in cancer risk in path_PMS2 carriers before 40 years of age and, although observation years were limited in older path_PMS2 carriers, LS-associated cancers other than endometrial and prostate were not observed.6-8 In this study we collected prospective data from a new large cohort of path_MMR carriers to validate previous findings from PLSD. We also updated information on the original cohort to ensure consistent classification of pathogenicity of MMR gene variants. We then combined both data sets, providing larger numbers that allowed us to derive more precise risk estimates for cancers in LS categorized by gene and gender

Cancer risk and survival in path _ MMR carriers by gene and gender up to 75 years of age: a report from the prospective Lynch Syndrome database

Background Most patients with path_MMR gene variants (Lynch syndrome (LS)) now survive both their first and subsequent cancers, resulting in a growing number of older patients with LS for whom limited information exists with respect to cancer risk and survival. Objective and design This observational, international, multicentre study aimed to determine prospectively observed incidences of cancers and survival in path_MMR carriers up to 75 years of age. Results 3119 patients were followed for a total of 24 475 years. Cumulative incidences at 75 years (risks) for colorectal cancer were 46%, 43% and 15% in path_MLH1, path_MSH2 and path_MSH6 carriers; for endometrial cancer 43%, 57% and 46%; for ovarian cancer 10%, 17% and 13%; for upper gastrointestinal (gastric, duodenal, bile duct or pancreatic) cancers 21%, 10% and 7%; for urinary tract cancers 8%, 25% and 11%; for prostate cancer 17%, 32% and 18%; and for brain tumours 1%, 5% and 1%, respectively. Ovarian cancer occurred mainly premenopausally. By contrast, upper gastrointestinal, urinary tract and prostate cancers occurred predominantly at older ages. Overall 5-year survival for prostate cancer was 100%, urinary bladder 93%, ureter 85%, duodenum 67%, stomach 61%, bile duct 29%, brain 22% and pancreas 0%. Path_PMS2 carriers had lower risk for cancer. Conclusion Carriers of different path_MMR variants exhibit distinct patterns of cancer risk and survival as they age. Risk estimates for counselling and planning of surveillance and treatment should be tailored to each patient's age, gender and path_MMR variant. We have updated our open-access website www.lscarisk.org to facilitate this

Cancer risk and survival in path_MMR carriers by gene and gender up to 75 years of age: a report from the Prospective Lynch Syndrome Database

Background Most patients with path_MMR gene variants (Lynch syndrome (LS)) now survive both their first and subsequent cancers, resulting in a growing number of older patients with LS for whom limited information exists with respect to cancer risk and survival. Objective and design  This observational, international, multicentre study aimed to determine prospectively observed incidences of cancers and survival in path_MMR carriers up to 75 years of age. Results 3119 patients were followed for a total of 24 475 years. Cumulative incidences at 75 years (risks) for colorectal cancer were 46%, 43% and 15% in path_MLH1, path_MSH2 and path_MSH6 carriers; for endometrial cancer 43%, 57% and 46%; for ovarian cancer 10%, 17% and 13%; for upper gastrointestinal (gastric, duodenal, bile duct or pancreatic) cancers 21%, 10% and 7%; for urinary tract cancers 8%, 25% and 11%; for prostate cancer 17%, 32% and 18%; and for brain tumours 1%, 5% and 1%, respectively. Ovarian cancer occurred mainly premenopausally. By contrast, upper gastrointestinal, urinary tract and prostate cancers occurred predominantly at older ages. Overall 5-year survival for prostate cancer was 100%, urinary bladder 93%, ureter 85%, duodenum 67%, stomach 61%, bile duct 29%, brain 22% and pancreas 0%. Path_PMS2 carriers had lower risk for cancer. Conclusion  Carriers of different path_MMR variants exhibit distinct patterns of cancer risk and survival as they age. Risk estimates for counselling and planning of surveillance and treatment should be tailored to each patient's age, gender and path_MMR variant. We have updated our open-access website www.lscarisk. org to facilitate this