Tools

snpXplrorer

snpXplorer is a free web-server application for exploring Single Nucleotide Polymorphisms (SNP) association statistics and to functionally annotate sets of SNPs. snpXplorer can superimpose association statistics from multiple studies and traits, and displays informative regional information including, among other sources, structural variations, eQTL and gene-expressions per tissue. snpXplorer can be used to compare levels of association across different traits, which may help the interpretation of variant consequences. The publication of snpXplorer is available here.

Go to snpXplorer

Normative Data From the Dutch 100-Plus Study: Neuropsychological Test Performance of Cognitively Healthy Centenarians

Normative data for neuropsychological tests are lacking in centenarians.  Therefore, we have generated norms for neuropsychological tests in a sample of cognitively healthy centenarians while taking sensory impairments into account.
Neuropsychological Test Performance of Cognitively Healthy Centenarians: Normative Data From the Dutch 100-Plus Study. Beker N, Sikkes SAM, Hulsman M, Schmand B, Scheltens P, Holstege H. J Am Geriatr Soc. 2019 Apr;67(4):759-767. 

Distribution of test scores. Boxplots represent raw test scores. BW, backward; DART, Dutch Adult Reading Test; FW, forward; IQ, intelligence quotient; MMSE, Mini-Mental State Examination; RBMT, Rivermead Behavioral Memory Test; TMT, Trail Making Test; VAT, Visual Association Test. 

We have added the red lines to indicate clinical cutoff scores we use in the Alzheimer Center of Amsterdam UMC for younger individuals. The blue lines indicate median scores of 85 years old females according to:

  • Cijferreeksen, based on n=100 (+65 years old)
    Lindeboom, 2001
  • Trail Making Test, based on n=478 (17-90 years old)
    Ben Schmand, Peter Houx † and Inge de Koning m.m.v
    Marleen Gerritsen, Martine Hoogman, Dino Muslimovic, Anne Rienstra, Rolf Saan, Sanne Schagen, Thelma Schilt, Joke Spikman & Mirjam van Tricht     
  • Category fluency and letterfluency, based on n=267-570 (17-90 years old)
    Ben Schmand, Peter Houx † and Inge de Koning m.m.v
    Marleen Gerritsen, Martine Hoogman, Dino Muslimovic, Anne Rienstra, Rolf Saan, Sanne Schagen, Thelma Schilt, Joke Spikman & Mirjam van Tricht
  •  RBMT verhaleb, based on n=344 (17-89 years old)
    Ben Schmand, Peter Houx † and Inge de Koning m.m.v
    Marleen Gerritsen, Martine Hoogman, Dino Muslimovic, Anne Rienstra, Rolf Saan, Sanne Schagen, Thelma Schilt, Joke Spikman & Mirjam van Tricht                                             

Published on the website of the section Neuropsycholgy. Dutch Institute of Psychologists, 2012.

Quality checks and corrections for short-read (exome) sequencing data

As part of the publication “Exome sequencing identifies rare damaging variants in ATP8B4 and ABCA1 as risk factors for Alzheimer’s Disease“, we have written a number of tools to perform quality checks and corrections for short-read (exome) sequencing data. This includes improvements to multi-allelic splitting, a tool to improve the representation of chimeric reads for variant calling,  a tool to calculate posterior probalities for variant calls, and a tool for variant annotation based on such posterior variant probabilities. More code will be added over time to this repository, which is available here.