Clinical Genetics 3

Genomics, population genetics and bioinformatics

Principal investigators

Dr J.T.den Dunnen, Prof.Dr. E. Bakker, Prof.Dr. M.H. Breuning Dr C. Ruivenkamp, Dr M. Losekoot, Dr. E. Bijlsma, drs A. van Haeringen

Aim and focus

The aim of this program is to develop and implement molecular technology for genome analysis for the purpose of diagnosis, screening, etiological research and treatment of monogenic and multifactorial disease. We are also working towards developing bioinformatics and statistical methods for analysis of data and literature. Current highlights are the development of new approaches to the detection of structural variation (deletions, duplications, insertion, transposition, translocation) and nucleotide variation in patients with congenital malformations and/or mental retardation and disorders of growth.

Position in international context

Several diagnostic technologies that have had worldwide impact, such as PTT, multicolor FISH and MAPH/MLPA have been pioneered. Our most recent innovation is that we were one of the first laboratories in the world to introduce microarray analysis for diagnostic purposes replacing microscopic karyotyping. This was effectuated August 1, 2008. 

Content / highlights / achievements

• Establishment of microarray analysis and MLPA as rapid, DNA-based diagnostic tests replacing karyotyping.
• Development of new diagnostic techniques for mutation detection in the Duchenne Muscular Dystrophy (DMD) and several other genes: MLPA and high resolution melting curve analysis (HRMA)
• Determination of the entire DNA sequence of a Dutch female
• Detection of deletions involving the IGF1 receptor as a cause of intrauterine and postnatal growth retardation and duplications of IGF1 as a cause of advanced growth
• First assessment of small CNV’s that show a wide variety of manifestations in patients indicating complex genotype – phenotype relationships
• Determination of fetal sex by detecting Y chromosomal DNA in maternal plasma during pregnancy   

Future themes

Our short term aim is to use the array analysis as a tool to discover genes involved in congenital malformations, mental retardation, growth disorders and inherited disease, and their implementation in routine diagnostics. Our long term goal is to contribute substantially to the introduction of next generation sequencing technology as a diagnostic tool in clinical practice.

Several approaches will be explored, such as hybrid selection and paired end sequencing.

A drawback of high resolution analysis of the genome is that there is an enormous variability, both in copy number and in the sequence. When analyzing the complete DNA sequence of a patient, the pathogenic change(s) looked for have to be singled out among millions of variants. By collecting results in databases on an international scale we will eventually be able to place each sequence variant within a spectrum going from entirely neutral through predisposing or contributing to clearly pathogenic.

In addition, we intend to focus on increased automation, workload reduction and upscaling of the molecular technologies from DNA isolation right up to data analysis.  

Cohesion within LUMC

• This is the area where clinical and human geneticists collaborate closest within the Center for Human and Clinical Genetics
• Analysis of congenital malformations and mental retardation in collaboration with the Departments of Pediatrics and Neurology
• Analysis of growth disorders (small, large, obese) with the Departments of Pediatrics, and Endocrinology
• Bioinformatics in collaboration with the Department of Medical Statistics and Molecular Epidemiology.
• We will be working in close collaboration with the Department of Obstetrics on the introduction of novel techniques for prenatal screening aimed at fetal DNA in the maternal circulation

Key publications

Boon EM, Schlecht HB, Martin P, Daniels G, Vossen RH, den Dunnen JT, Bakker B, Elles R (2007). Y chromosome detection by Real Time PCR and pyrophosphorolysis-activated polymerisation using free fetal DNA isolated from maternal plasma. Prenat Diagn 27(10):932-7.
IF 1.3

Bruder CE, Piotrowski A, Gijsbers AA, Andersson R, Erickson S, de Ståhl TD, Menzel U, Sandgren J, von Tell D, Poplawski A, Crowley M, Crasto C, Partridge EC, Tiwari H, Allison DB, Komorowski J, van Ommen GJ, Boomsma DI, Pedersen NL, den Dunnen JT, Wirdefeldt K, Dumanski JP (2008). Phenotypically concordant and discordant monozygotic twins display different DNA copy-number-variation profiles. Am J Hum Genet. 2008 Mar;82(3):763-71.
IF 12.6

Cotton RG; 2006 Human Variome Project, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, Cotton RG, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G, Watson M (2007). Recommendations of the 2006 Human Variome Project meeting. Nat Genet 39(4):433-6.
IF 25.5

Dauwerse JG, de Vries BB, Wouters CH, Bakker E, Rappold G, Mortier GR, Breuning MH, Peters DJ. A t(4;6)(q12;p23) translocation disrupts a membrane-associated O-acetyl transferase gene (MBOAT1) in a patient with a novel brachydactyly-syndactyly syndrome. Eur J Hum Genet. 2007; 15(7):743-51.
IF 4.0

Gijsbers AC, Bijlsma EK, Weiss MM, Bakker E, Breuning MH, Hoffer MJ, Ruivenkamp CA. A 400kb duplication, 2.4Mb triplication and 130kbduplication of 9q34.3 in a patient with severe mental retardation. Eur J Med Genet. 2008; 51(5):479-87.
IF 1.9

Kriek M, Knijnenburg J, White SJ, Rosenberg C, den Dunnen JT, van Ommen GJ, Tanke HJ, Breuning MH, Szuhai K (2007). Diagnosis of genetic abnormalities in developmentally delayed patients: a new strategy combining MLPA and array-CGH. Am J Med Genet A 143(6): 610-4.
IF 2.4

Kriek M, White SJ, Szuhai K, Knijnenburg J, van Ommen GJ, den Dunnen JT, Breuning MH. (2006) Copy number variation in regions flanked (or unflanked) by duplicons among patients with developmental delay and/or congenital malformations; detection of reciprocal and partial Williams-Beuren duplications. Eur J Hum Genet 14(2):180-9.
IF 4.0

Kriek M, White SJ, Bouma MC, Dauwerse HG, Hansson KB, Nijhuis JV, Bakker B, van Ommen GJ, den Dunnen JT, Breuning MH. Genomic imbalances in mental retardation. J Med Genet. 2004; 41(4): 249-55.
IF 5.5

White SJ, Aartsma-Rus A, Flanigan KM, Weiss RB, Kneppers AL, Lalic T, Janson AA, Ginjaar HB, Breuning MH, den Dunnen JT. Duplications in the DMD gene. Hum Mutat 2006; 27: 938-45.      IF 6.2 White SJ, Vink GR, Kriek M, Wuyts W, Schouten J, Bakker B, Breuning MH, den Dunnen JT. Two-color multiplex ligation-dependent probe amplification: detecting genomic rearrangements in hereditary multiple exostoses. Hum Mutat 2004; 24: 86-92.
IF 6.2