Investigation of a patient with a partial trisomy 16q including the fat mass and obesity associated gene (FTO): fine mapping and FTO gene expression study

Abstract

A female patient with a partial trisomy 16q was described previously. Her clinical characteristics included obesity, severe anisomastia, moderate to severe mental retardation, attention deficit hyperactivity disorder, dysmorphic facies, and contractions of the small joints. In this article, we describe a more detailed analysis of the genetic anomaly in this patient. We were particularly interested in the involvement of the fat mass and obesity associated gene (FTO) in her duplication. Single nucleotide polymorphisms in FTO have been associated with obesity. The breakpoints of the duplication were precisely mapped using high-resolution oligonucleotide array comparative genomic hybridization (CGH). We found that the duplication spans 11.45 Mb on 16q11.2 to 16q13 and it includes FTO. The increased copy number of FTO was confirmed with a qPCR on genomic DNA of the patient. We investigated the influence of the increased FTO copy number on FTO gene expression in immortalized lymphocytes from the patient using qPCR. No evidence of increased FTO expression was detected in the patient's lymphocytes. We discuss these findings and we review clinical findings in patients with overlapping 16q duplications to determine the relationship between increased FTO copy number and obesity. Our review suggests that duplication of the FTO gene does not necessarily result in obesity.

Figure 1

Graphical summary of results of oligonucleotide array comparative genomic hybridization for chromosome 16. The horizontal axis represents the test/reference intensity ratio after normalization and log₂ transformation. Black dots correspond to probes with log₂ ratios near zero; red dots correspond to probes with positive ratios (i.e. increased copy number); and green dots correspond to probes with negative ratios (i.e. decreased copy number). The blue bars on the extreme left and right side of the figure mark the aberrant regions. The patient has a large duplication of 16q11.2 to 16q13. In addition, she has 25 smaller aberrations (17 gains; 8 losses) dispersed over chromosome 16. The smallest aberrations are not visible in this figure. [Color figure can be viewed in the online issue, which is available at www.interscience.wiley.com].

Figure 2

FTO copy number in genomic DNA of the patient and three healthy controls from the Centre d'Étude du Polymorphisme Humain (CEPH). Copy numbers are relative to CEPH 1331-01, which is an arbitrary choice. Relative FTO quantities were normalized to the relative quantity of reference genes ZNF80 and SDC4. Error bars represent standard deviations.

Figure 3

FTO expression level in immortalized lymphocytes of the patient (p) and four controls (c1-4) determined by qPCR. Gene quantities were calculated relative to the average Ct. Data were normalized to transcript levels of RPL13a and B2M. FTO expression was measured with primers in exon 2 and 3 of the gene (light bars) and with primers in exon 7 and 8 (dark bars). Expression levels of controls are based on duplicate measurements of two independent cDNAs. Expression level of the patient is based on duplicate measurements of three independent cDNAs. Error bars represent standard errors of the mean of two (controls) and three (patient) cDNA samples.

Figure 4

Obesity in patients with 16q duplications that overlap with the duplication of our patient. An ideogram and a ruler with positions in megabases are included at the top of the figure. FTO is located at position 52.3–52.7 Mb. Shades of grey represent the precision of the method that was used to determine the extent of the duplication (see legend). Further details about the patients are provided in Supplementary information 6. No clinical details were provided for the patients of Mascarello and Hubbard [1991] and Ren et al. [2005], so these were excluded from the figure.