Transmission of a Novel Imprinting Center Deletion Associated With Prader-Willi Syndrome Through Three Generations of a Chinese Family: Case Presentation, Differential Diagnosis, and a Lesson Worth Thinking About

Abstract

Prader-Willi syndrome (PWS) is a complex genetic syndrome caused by the loss of function of genes in 15q11-q13 that are subject to regulation by genomic imprinting and expressed from the paternal allele only. The main clinical features of PWS patients are hypotonia during the neonatal and infantile stages, accompanied by delayed neuropsychomotor development, hyperphagia, obesity, hypogonadism, short stature, small hands and feet, mental disabilities, and behavioral problems. However, PWS has a clinical overlap with other disorders, especially those with other gene variations or chromosomal imbalances but sharing part of the similar clinical manifestations with PWS, which are sometimes referred to as Prader-Willi syndrome-like (PWS-like) disorders. Furthermore, it is worth mentioning that significant obesity as a consequence of hyperphagia in PWS usually develops between the ages of 1 and 6 years, which makes early diagnosis difficult. Thus, PWS is often not clinically recognized in infants and, on the other hand, may be wrongly suspected in obese and intellectually disabled patients. Therefore, an accurate investigation is necessary to differentiate classical PWS from PWS-like phenotypes, which is imperative for further treatment. For PWS, it is usually sporadic, and very rare family history and affected siblings have been described. Here, we report the clinical and molecular findings in a three-generation family with a novel 550-kb microdeletion affecting the chromosome 15 imprinting center (IC). Overall, the present study finds that the symptoms of our patient are somewhat different from those of typical PWS cases diagnosed and given treatment in our hospital. The familial occurrence and clinical features were challenging to our diagnostic strategy. The microdeletion included a region within the complex small nuclear ribonucleoprotein polypeptide protein N (SNRPN) gene locus encompassing the PWS IC and was identified by using a variety of techniques. Haplotype studies suggest that the IC microdeletion was vertically transmitted from an unaffected paternal grandmother to an unaffected father and then caused PWS in two sibling grandchildren when the IC microdeletion was inherited paternally. Based on the results of our study, preimplantation genetic diagnosis (PGD) was applied successfully to exclude imprinting deficiency in preimplantation embryos before transfer into the mother's uterus. Our study may be especially instructive regarding accurate diagnosis, differential diagnosis, genetic counseling, and PGD for familial PWS patients.

Keywords: Prader–Willi syndrome; Prader–Willi-like syndrome; familial transmission; imprinting center; microdeletion.

FIGURE 1

Clinical features of our patient with Prader–Willi syndrome (PWS) (2 days after birth). (A) Non-invasive respiratory support with positive end expiratory pressure was used for the treatment of respiratory distress. Overall appearance of the boy indicated no significant difference between the patient and normal infants. Note muscular hypotonia and abnormal position of the hands and feet. (B) Facial features of the boy (narrow forehead, fair eyebrow, bilateral epicanthus, flat nose, big nostrils, and thin upper lip). (C) Overall appearance of abnormal position of the hands and feet. (D) Abnormal position of the fingers with thumbs adducted under index and middle fingers, flexed hands and wrists, persistently clenched hands and arachnodactyly. (E) Small feet and toes. (F) Genital hypoplasia with slight maldescent of the left testis.

FIGURE 2

Copy number variation (CNV) sequencing reveals a de novo 500-kb heterozygous deletion of 15q11.2 (chr15: 24,932,524–25,482,598) in the paternal grandmother, the father, and the patient. The deletion encompasses five Online Mendelian Inheritance in Man (OMIM) genes including SNRPN, SNHG14, PWAR6, SNORD115, and SNORD116 (highlighted in pink box).

FIGURE 3

Copy number and methylation patterns generated using Methylation-Specific Multiplex Ligation-dependent Probe Amplification B2 kit (MS-MLPA-B2). The Prader–Willi syndrome/Angelman syndrome (PWS/AS) kit contains 48 probes for copy number detection and methylation status analysis that are specific to regions in or near the PWS/AS critical region on chromosome 15q11-q13. The left and right columns display the results of copy number and methylation pattern, respectively. In the left column, copy number peak ratios are determined by comparing patient with normal control (2 copies/2 copies = 1.0). The figure reveals deletion (showing a copy number of 1) in 15 probes in and around the SNRPN region (highlighted in red dots) in the paternal grandmother, the father, and the patient. Meanwhile, the normal control has a normal copy number of 2 for all analyzed gene fragments of chromosome 15. The methylation probes were designed to hybridize to maternally imprinted loci, shown in the right column. When compared to the normal control, each of the four probes within the deleted region has a ratio of around 0.5. In this family, the paternal grandmother and the father display an abnormal methylation pattern (ratio = 0) in the SNRPN region due to complete loss on the maternal chromosome 15, while the patient displays the typical PWS methylation pattern (ratio = 1) in the four SNRPN probes due to complete loss on his paternal chromosome 15. UBE3A exon 1 and one other digestion control probe were used during the methylation analysis. These results indicate that in the paternal grandmother and the father, the paternal allele is present, and the deletion is maternal in origin, which explains their absence of clinical symptoms. In contrast, the child displays an abnormal methylation pattern in the four methylation-sensitive fragments digested in the SNRPN region due to loss on his paternal chromosome 15.

FIGURE 4

Chromosome microarray analysis (CMA) demonstrating deletion of 15q11.2 in the paternal grandmother, the father, and the patient. The novel copy number variation (CNV) at the loci (chr15: 24,966,348–25,364,551) is of approximately 398 kb in heterozygous state, surrounding the SNRPN gene.

FIGURE 5

Prader–Willi syndrome (PWS) and Angelman syndrome (AS) domain in proximal chromosome 15q11-q13. The positions of genes (oval) in PWS, AS, and the IC are illustrated. CEN, centromere; Tel, telomere; IC, PWS imprinting center (red rectangle); BP, breakpoint; *the breakpoint of the proband.