Prader–Willi syndrome (PWS) is a genetic disorder with a clinical profile of obesity, intellectual disability, and short stature. It can be caused in several ways. Most common is a deletion on the paternal copy of chromosome 15, but it can also be caused by an epigenetic imprinting disorder and uniparental disomy, an event in which the affected child receives two copies of the maternal chromosome 15. A child with PWS comes to your clinic for a diagnosis of the molecular basis for this condition. The gel below shows the results of testing with short tandem repeats (STRs) from the region of chromosome 15 associated with the disorder.
Based on your interpretation of the data, what is the cause of PWS in this case? Explain your reasoning. 

Verified step by step guidance

1. Step 1: Understand the genetic causes of Prader–Willi syndrome (PWS). PWS can result from three main mechanisms: a deletion on the paternal chromosome 15, maternal uniparental disomy (UPD) where both chromosome 15 copies come from the mother, or an imprinting defect affecting gene expression without changes in DNA sequence.
2. Step 2: Analyze the STR (short tandem repeat) gel results. STR markers are highly polymorphic DNA sequences used to determine the parental origin of chromosomes. Look for the pattern of bands representing alleles inherited from each parent. Typically, a child inherits one allele from the mother and one from the father at each STR locus.
3. Step 3: Identify whether the child has alleles from both parents or only from one parent. If the child shows only maternal alleles at all tested STR loci on chromosome 15, this suggests maternal uniparental disomy. If the child has one maternal and one paternal allele but a deletion is present, the paternal allele would be missing or altered.
4. Step 4: Compare the child's STR pattern to the parents' patterns. Confirm if the child’s alleles match only the mother’s alleles (indicating UPD) or if there is a missing paternal allele (indicating deletion). Also, consider if the imprinting pattern could explain the phenotype if both alleles are present but expression is abnormal.
5. Step 5: Conclude the molecular cause of PWS in this case based on the STR analysis. Use the presence or absence of paternal alleles and the pattern of inheritance to determine if the cause is a deletion, maternal UPD, or imprinting defect.

Key Concepts

Genomic Imprinting

Genomic imprinting is an epigenetic phenomenon where certain genes are expressed in a parent-of-origin-specific manner. In Prader–Willi syndrome, the paternal copy of chromosome 15 must be active, while the maternal copy is normally silenced. Disruption of this imprinting pattern, such as loss of paternal gene expression, leads to the disorder.

Uniparental Disomy (UPD)

Uniparental disomy occurs when both copies of a chromosome are inherited from one parent instead of one from each. In PWS, maternal UPD means the child has two maternal chromosome 15s and no paternal copy, causing loss of paternal gene expression and resulting in the syndrome.

Short Tandem Repeat (STR) Analysis

STR analysis is a molecular technique used to examine specific repetitive DNA sequences to determine genetic inheritance patterns. In PWS diagnosis, STR markers on chromosome 15 help identify deletions, UPD, or imprinting defects by comparing the child's alleles to those of the parents.