Cytogenetics. 15q11-13 can be an intimidating region, even for many seasoned genetics professionals. Several factors contribute to this, including a complex genomic architecture, genomic imprinting, an acrocentric chromosome, and several genes critical to neurological function. For today’s blog post, we’ll try to unravel some of its complexity to make interpretation of copy number variants (CNVs) in this area clearer.
Nomenclature. When referring to a region in the genome, we start with the chromosome. Chromosomes are numbered 1-22, X, or Y. Next is the arm: p or q. P stands for the short arm and q stands for the long arm (I always think of these as the “petit” and “queue” arms, French for short and tail respectively, but apparently the reason for the naming is more complex). Next, we have bands and sub-bands. Over time, as karyotype staining techniques got better, we were able to divide originally discovered bands into smaller and smaller regions, like dividing a state into counties, then townships, then cities, and finally neighborhoods. For example, what may have originally been band “2” may have been divided into 3 more bands, or “21”, “22”, and “23”. When you say these, pronounce each number separately, as “two two” is not referring to the 22nd band, but rather the second sub-band in band 2. The region 15q11.2 is therefore pronounced “fifteen q one one point two”.
Breakpoints. One of the first things to know about 15q11-13 is that it has 5 segmental duplication-mediated breakpoints (BPs). Segmental duplications, or seg dups, are repetitive regions that can sometimes misalign during DNA replication. This misalignment can result in duplications, deletions, and inversions between the affected misaligned breakpoints. Recurrent copy number variants (e.g., 22q11.2 deletion syndrome, 16p11.2 deletion syndrome, etc.) are typically mediated by segmental duplications. Chromosome 15q11-13, having 5 breakpoints, is particularly complex because CNVs can start and stop at any of the 5 breakpoints. For example, you can have a CNV from BP1 to BP2, BP2 to BP4, BP1 to BP5, etc., for a total of 10 combinations. The specific region affected is important, as the genes contained in those regions vary in their clinical significance. UBE3A and GABRB3 are both critical genes for brain functioning and are both between BP2 and BP3. CNVs affecting this region are generally considered pathogenic, even if the specific disorder changes based on imprinting (see below). However, CNVs affecting the region between BP1 and BP2 have uncertain clinical significance, and are found commonly in the general population. Larger affected regions, such as a CNVs spanning BP1 through BP5, are likely more clinically severe than smaller ones that only span BP2 and BP3.
Imprinting. 15q11-13 is well-known among medical and genetic counseling students for the phenomenon of imprinting, which certainly throws another wrench into this region. Several genes (but not all!) in this region are imprinted, meaning that the parent of origin affects whether genes are methylated (turned off) or unmethylated (turned on). The imprinting occurs in a sperm or egg before fertilization. Most people learn about this phenomenon in reference to Angelman syndrome and Prader Willi syndrome. These disorders are distinct clinical entities but are caused by loss of the same region (between breakpoints 2 and 3 in 15q11-13). For example, the gene UBE3A is only actively expressed in the brain when it originates from the maternal copy (i.e. the paternal copy is methylated, or silenced). Angelman syndrome results from an absence of UBE3A, which may occur when there is inheritance only of the paternal copy of this gene (for example, when the maternal copy has been deleted). On the other hand, Prader Willi syndrome occurs when you have inherited only the maternal copy of this same region (e.g. if the paternal copy of the region has been deleted). Both disorders may also occur in uniparental disomy, where an individual inherits both copies of a chromosome from the same parent. In the latter case, the individual has two copies of each gene, but they have several genes that are silenced on both copies, and therefore they are still missing the corresponding proteins. They can also end up with increased amounts of other proteins because both copies of the corresponding genes are unmethylated and active, instead of one off and one on. This can also result in pathogenicity with abnormal brain functioning and epilepsy. Dup15q syndrome is caused by having at least one additional maternal copy of the region between breakpoints 2 and 3. Additional paternal material can cause a milder form of the disorder
Total copy number. Another factor to consider with copy number gains is the total number of copies an individual has. While deletions typically lead to a copy number of 1 (with 0 copies presumably incompatible with life), regions of 15q11-13 can have copy numbers of 4 or even 6. It is likely that the greater the copy number, the more severe the clinical disorder.
Chromosomal rearrangements. Increased copy number in this region can involve yet another layer of complexity: interstitial gains vs supernumerary marker chromosomes. Interstitial means the gain is contained within the original chromosome, while a supernumerary marker chromosome refers to an additional nonstandard chromosome containing the gained material. In Dup15q syndrome, this is commonly a chromosome containing the satellite region from the p arm at each end and two copies of 15q11-13 going forwards then backwards (p arm > centromere > 15q11, 15q12, 15q13 > 15q13, 15q12, 15q11 > centromere > p arm). Isodicentric refers to a chromosome containing 2 centromeres and having two mirrored genomic regions. Technically, these chromosomes are pseudodicentric, as one of the centromeres is usually deactivated and the genomic regions are not always mirrored (see below). However, for conciseness, isodicentric 15 or idic 15 is a common name for this cause of Dup15q syndrome.
Asymmetry. With the increase in microarrays that can more precisely determine breakpoints of a CNV, it has become increasingly common to see asymmetrical CNVs in 15q11-13. On a microarray, this will show up as something like 15q11-15q13.1 x 3, 15q13.1-15q13.2 x 4. At first glance, this may look like two independent CNVs, but most commonly these are part of the same complex gain and rearrangement. This can happen when the two mirrored sections (i.e. the one going forward and one going in reverse) of a marker chromosome are not the same size. You can end up having one side that includes a larger region (for example, extending to BP4 while the other extends to BP3) which means there just a single copy of the non-overlapping section in the middle of the marker chromosome, before the inversion happens (in this example, BP3-BP4). In the marker chromosome, this would look like p arm > centromere > 15q11, 15q12, 15q13.1, 15q13.2 > 15q13.1, 15q12, 15q11 > centromere > p arm. In this case, there is only one additional copy of the region between 15q13.1 to 15q13.2 (roughly equivalent to BP3-4), while there are two additional copies of everything else.
Mosaicism. Marker chromosomes are unstable and can be lost during cell division. This can lead to mosaicism in individuals that have Dup15q due to idic 15. A lower level of mosaicism is associated with milder disease, though this depends on the exact distribution of which tissues have the extra genetic material. Microarrays, while generally good at identifying levels of mosaicism, are not always accurate in Dup15q syndrome when there is mosaicism for 4 vs 2 copies. If present in roughly equal distributions, a microarray may report a ratio consistent with 3 copies in all cells. Karyotypes, though they only examine a few cells, are a more definitive test for detecting the presence or absence of mosaicism in this case.
What you need to know. Chromosome 15q11-13 contains 5 breakpoints, making it prone to complex chromosome rearrangements including deletions as well as copy number gains of 1 or more. It also contains imprinted genes, further complicating the interpretation of genetic findings as we must consider the parental origin of the altered genetic material before making a diagnosis. Asymmetry and mosaicism can be common when a copy number gain involves a marker chromosome. Careful review of microarray, karyotype, and methylation studies are therefore important for determining the specific diagnosis in a patient and developing a clinical management plan. For details on the clinical phenotypes and management of Dup15q syndrome, stay tuned for our next post!