Lien Heyrman

Multiplex Amplicon Quantification (MAQ), a fast and efficient method for the simultaneous detection of copy number alterations in neuroblastoma

BackgroundCancer genomes display characteristic patterns of chromosomal imbalances, often with diagnostic and prognostic relevance. Therefore assays for genome-wide copy number screening and simultaneous detection of copy number alterations in specific chromosomal regions are of increasing importance in the diagnostic work-up of tumors.ResultsWe tested the performance of Multiplex Amplicon Quantification, a newly developed low-cost, closed-tube and high-throughput PCR-based technique for detection of copy number alterations in regions with prognostic relevance for neuroblastoma. Comparison with array CGH and the established Multiplex Ligation-dependent Probe Amplification method on 52 neuroblastoma tumors showed that Multiplex Amplicon Quantification can reliably detect the important genomic aberrations.ConclusionMultiplex Amplicon Quantification is a low-cost and high-throughput PCR-based technique that can reliably detect copy number alterations in regions with prognostic relevance for neuroblastoma.

Response to Zhang et al. (2005) loss-of-function mutation in tryptophan hydroxylase-2 identified in unipolar major depression. Neuron 45, 11-16 [2] (multiple letters)

Zhang et al. reported a naturally occurring Arg441His missense variant of the human tryptophan hydroxylase-2 (TPH2) gene. The His441 allele was reported to be more abundant in a cohort of 87 depressed patients compared to 219 controls (Zhang et al., 2005). The frequency of His441 was higher in the depressed patients (0.06), among whom there were two His/His homozygotes and seven heterozygotes. His441 was also observed among the 219 controls (allele frequency 0.009), among whom one His/His homozygote and two Arg/His heterozygotes were detected. This reported association with depression is of note in the context of the effect of this substitution in reducing serotonin synthesis by approximately 80% in a heterologous expression assay in a rat cell line (Zhang et al., 2005) and through the observation of the role of TPH2 variants as genetic predictors of depression (Zill et al., 2004) and response to antidepressants (Peters et al., 2004). The authors of this letter represent three independent groups of investigators who have resequenced the relevant region of TPH2 in some 779 unrelated individuals (Table 1), including 403 with major depression (ages 19–74, n = 21 > 60 years). In addition, another 1740 individuals with major depression (from the STAR*D study, ages 18–75, n = 121 > 60 years) were genotyped (Table 1). The sequenced and genotyped individuals represent five ethnic populations. Psychiatric assessment was accomplished using semistructured psychiatric interviews: NIAAA, SCID or SADS-L; NIMH and UCSF, SCID-I/P. Major depression was diagnosed by DSMIII-R or DSM-IV criteria, and a DSM-IV checklist was used for the STAR*D samples. Additional descriptions of individual data sets have been reported (Nielsen et al., 1998; Robin et al., 1997; Roy, 2003; Peters et al., 2004; Rush et al., 2004). All data were collected following informed consent and under human research protocols approved by IRBs of the respective institutions. For direct sequencing, genomic DNA was amplified by PCR with primers encompassing the Arg441His variant, sequenced using the BigDye Terminator V3.1 (Applied Biosystems Inc., Foster City, CA) and analyzed on ABI 3100 or 3730 sequencers. For genotyping, assays were performed using 50-nuclease assay (TaqMan, ID # PMT06-55) and analyzed on an LJL plate reader (Molecular Devices, Sunnyvale, CA). 20% of the

Detailed analysis of the serotonin transporter gene (SLC6A4) shows no association with bipolar disorder in the Northern Swedish population.

Through active reuptake of serotonin into presynaptic neurons, the serotonin transporter (5‐HTT) plays an important role in regulating serotonin concentrations in the brain, and it is the site of binding for tricyclic antidepressants and selective serotonin reuptake inhibitors (SSRIs). Therefore it has been hypothesized that this transporter is involved in the etiology of bipolar (BP) disorder. Inconsistent association study results for the SLC6A4 gene encoding 5‐HTT reported in literature emphasize the need for more systematic and detailed analyses of this candidate gene. We performed an extensive analysis of SLC6A4 on DNA of 254 BPI patients and 364 control individuals from a Northern Swedish isolated population. This analysis consisted of a HapMap LD‐based association study including three widely investigated polymorphisms (5‐HTTVNTR, 5‐HTTLPR, and rs3813034), a copy‐number variation (CNV) analysis and a mutation analysis of the complete coding sequence and the 3′‐UTR of SLC6A4. No single marker showed statistically significant association with BPI, nor did any of the haplotypes. In the mutation analysis 13 novel variants were detected, including 2 amino acid substitutions M389V and I587L, but these are probably not implicated in risk for BP. No deletions or duplications were detected in the CNV analysis. We conclude that variation in the SLC6A4 gene or its regulatory regions does not contribute to the susceptibility for BP disorder in the Northern Swedish population.

Evidence for the involvement of the glucocorticoid receptor gene in bipolar disorder in an isolated northern Swedish population

Ceulemans S, De Zutter S, Heyrman L, Norrback K‐F, Nordin A, Nilsson L‐G, Adolfsson R, Del‐Favero J, Claes S. Evidence for the involvement of the glucocorticoid receptor gene in bipolar disorder in an isolated northern Swedish population. Bipolar Disord 2011: 13: 614–623.

Copy Number Variations in DISC1 and DISC1-Interacting Partners in Major Mental Illness

Robust statistical, genetic and functional evidence supports a role for DISC1 in the aetiology of major mental illness. Furthermore, many of its protein-binding partners show evidence for involvement in the pathophysiology of a range of neurodevelopmental and psychiatric disorders. Copy number variants (CNVs) are suspected to play an important causal role in these disorders. In this study, CNV analysis of DISC1 and its binding partners PAFAH1B1, NDE1, NDEL1, FEZ1, MAP1A, CIT and PDE4B in Scottish and Northern Swedish population-based samples was carried out using multiplex amplicon quantification. Here, we report the finding of rare CNVs in DISC1, NDE1 (together with adjacent genes within the 16p13.11 duplication), NDEL1 (including the overlapping MYH10 gene) and CIT. Our findings provide further evidence for involvement of DISC1 and its interaction partners in neuropsychiatric disorders and also for a role of structural variants in the aetiology of these devastating diseases.