Update of the EMQN/ACGS Best Practice Guidelines for Molecular Analysis of Prader-Willi and Angelman Syndromes

European Journal of Human Genetics (2019) 27:1326–1340 https://doi.org/10.1038/s41431-019-0435-0

POLICY

Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman syndromes

1 1 2 3 2,4 1 Jasmin Beygo ● Karin Buiting ● Simon C. Ramsden ● Rachael Ellis ● Jill Clayton-Smith ● Deniz Kanber

Received: 31 December 2018 / Revised: 20 March 2019 / Accepted: 7 May 2019 / Published online: 24 June 2019 © The Author(s) 2019. This article is published with open access

Abstract This article is an update of the best practice guidelines for the molecular analysis of Prader-Willi and Angelman syndromes published in 2010 in BMC Medical Genetics [1]. The update takes into account developments in terms of techniques, differential diagnoses and (especially) reporting standards. It highlights the advantages and disadvantages of each method and moreover, is meant to facilitate the interpretation of the obtained results - leading to improved standardised reports.

Clinical background obsessive-compulsive characteristics) is common. Hypogo- 1234567890();,: 1234567890();,: nadism is present in both males and females, and manifests Prader-Willi syndrome (PWS, #176270) is characterised by as genital hypoplasia, incomplete pubertal development, and severe hypotonia and feeding difficulties in early infancy, in most, infertility. Short stature is common; characteristic followed in later infancy or early childhood by excessive facial features, strabismus, and scoliosis are often present, eating and gradual development of morbid obesity (unless and non-insulin-dependent diabetes mellitus often occurs in eating is controlled by dietary restriction or behaviour obese individuals. Consensus diagnostic clinical criteria for modification). Motor milestones and language development PWS have been developed [2, 3], but genetic testing is are delayed. All individuals have some degree of cognitive necessary for confirmation of the clinical diagnosis and for impairment, although some will have an IQ within the determination of the recurrence risk. normal range. A distinctive behavioural phenotype (with Angelman syndrome (AS, #105830) is characterised by temper tantrums, stubbornness, manipulative behaviour, and severe developmental delay, absent or severely limited speech, gait ataxia and/or tremulousness of the limbs, and a unique behaviour with a happy demeanour that includes These authors contributed equally: Jasmin Beygo, Deniz Kanber frequent and sometimes inappropriate laughter, smiling, and excitability. In addition, microcephaly and seizures are Supplementary information The online version of this article (https:// doi.org/10.1038/s41431-019-0435-0) contains supplementary common. Affected individuals usually have a characteristic material, which is available to authorized users. electroencephalography (EEG) appearance with striking high-voltage activity. Developmental delay is first noted at * Jasmin Beygo around 6 months of age; however, the unique clinical fea- [email protected] tures of AS may not manifest until after one year of age, and * Deniz Kanber [email protected] it can take several years before the correct clinical diagnosis is obvious. Consensus clinical diagnostic criteria have also been developed for AS [4, 5]. Again, for confirmation of the 1 Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Essen, Germany clinical diagnosis and determination of the recurrence risk genetic testing is required. 2 Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK 3 Department of Medical Genetics, Yorkhill NHS Trust, Yorkhill Genetic background Hospital, Glasgow G3 8SJ, UK 4 Division of Evolution and Genomic Sciences School of Biological The proximal long arm of human chromosome 15 Sciences University of Manchester, Manchester, UK (15q11q13) contains a cluster of imprinted genes, which are Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1327

Imprinted domain

NIPA1NIPA2CYFIP1TUBGCP5 MKRN3MAGEL2NDN PWRN2PWRN1NPAP1u1B u1A SNURF-SNRPNSNORD107/64/108SNORD109ASNORD116 SNORD115SNORD109BUBE3A ATP10A GABRB3GABRA5GABRG3 OCA2 HERC2

pat cen tel mat IC D15S541 D15S543

BP1 BP2 BP3 class I deletion class II deletion Fig. 1 Overview of the imprinted region 15q11q13. Schematic over- boxes, biallelically expressed genes and arrow heads represent the view of the genes located within the PWS and AS critical region on orientation of transcription. IC imprinting centre, BP common break- chromosome 15q11q13. Upper part - paternal allele (pat), lower part - point cluster region, cen centromeric, tel telomeric. Modified from maternal allele (mat). Blue boxes/vertical lines represent paternally Ramsden et al. [1] expressed genes/snoRNAs; red box, maternally expressed gene; black under the control of an imprinting centre (IC) [6]. Some of AS is caused by loss of function of the maternally these genes are expressed from the paternal or maternal expressed gene UBE3A in neuronal cells. The major disease chromosome only. PWS arises from the loss of function of mechanisms are similar to those in PWS being either a large paternally expressed genes in 15q11q13. This loss can be a deletion of 15q11q13 on the maternal chromosome that is in result of either a large deletion of this region on the paternal most cases de novo, a paternal UPD or an ID affecting the allele that is in most cases de novo, maternal uniparental maternal chromosome [13, 14]. Again, the ID can arise due disomy (UPD) of chromosome 15 or the silencing of the to an IC deletion (see below) or without an underlying paternal allele by an imprinting defect (ID) on the paternal change in the DNA sequence. Furthermore, in more than chromosome [7]. Such an ID can be due to an IC deletion 40% of patients with AS and an ID without an IC deletion, (see below) or occur without an underlying change in the the ID is present in a subset of cells only (somatic mosai- DNA sequence. So far, several genes preferentially or cism), indicating that it occurred after fertilisation [14, 15]. exclusively expressed from the paternal chromosome have Those patients sometimes present with a phenotype been described: MKRN3, MAGEL2, NDN, PWRN1, NPAP1 resembling that of PWS. On the other hand in PWS only (previously C15orf2), SNURF-SNRPN and several C/D box very rare patients have been described with a mosaic ID small nucleolar RNA (snoRNA) genes (see Fig. 1). At least [16, 17]. three of these genes SNRPN, MAGEL2 and NDN, have In addition, disease causing variants (point mutations) in differentially methylated CpG islands in their promoter the imprinted E6-AP ubiquitin-protein ligase gene (UBE3A) regions that are methylated on the maternal chromosome cause AS [18–20]. Imprinted UBE3A expression is restric- leading to silencing of the maternal allele (new nomen- ted to brain cells where expression is exclusively from the clature: SNURF:TSS-DMR, MAGEL2:TSS-DMR and maternal chromosome and disruption of expression of this NDN:TSS-DMR [8]). The SNURF:TSS-DMR is a primary gene is the major cause of the disease. In contrast to PWS, DMR where the methylation imprint is already set in the ~15% of patients with the clinical diagnosis of AS have a female germline. On the other hand, the MAGEL2:TSS- genetic defect of unknown aetiology. DMR and the NDN:TSS-DMR are secondary DMRs where The IC has been defined using microdeletions in a small the methylation imprint is set postzygotically (see section number of patients with PWS or AS and an ID, who have “Prenatal diagnosis”, Supplementary Fig. 1). small, atypical deletions. It has a bipartite structure with two Whereas most of the snoRNA genes are present as single critical regions, the AS-SRO (shortest region of deletion genes (SNORD64, SNORD107, SNORD108, SNORD109A overlap; AS-IC element) and the PWS-SRO (PWS-IC ele- and SNORD109B), the two snoRNA genes SNORD116 and ment [6]). By analysing a very large series of PWS and AS SNORD115 are present in 24 and 47 gene copies, respec- patients with an ID it has been shown that the vast majority tively. It has been demonstrated that deficiency of of IDs have occurred spontaneously in the absence of DNA SNORD116 snoRNAs causes the key characteristics of the sequence changes [16]. In particular, disease causing var- PWS phenotype [9–12], however one or more additional iants within the IC have not been detected to genes in the region are likely to contribute. date [16, 21, 22]. Nevertheless, the presence or absence of 1328 J. Beygo et al.

Table 1 Molecular defects and recurrence risks in PWS Genetic defect Proportion of cases [7] Recurrence risk

De novo deletion of 15q11q13 on the paternal 70–75% <1%a chromosome Maternal uniparental disomy (UPD) of 25–30% <1%b chromosome 15 Imprinting defects (without an imprinting centre 1% <1% deletion) Imprinting centre deletion ≈10–15% of patients with an 50% (if present in a non-mosaic state in the imprinting defect father) aIf paternal karyotype is normal bIf parental karyotypes are normal

Table 2 Molecular defects and recurrence risks in AS Genetic defect Proportion of cases [13] Recurrence risk

De novo deletion of 15q11q13 on the maternal 75% <1%a chromosome Paternal uniparental disomy (UPD) of 1–2% <1%b chromosome 15 Imprinting defect (without an imprinting centre 3% <1% deletion) Imprinting centre deletion ≈10–15% of patients with an 50% (if present in a non-mosaic state in the imprinting defect mother) UBE3A mutation 5–10% 50% (if present in a non-mosaic state in the mother) No identifiable molecular abnormality 10–15% Unknown (up to 50%) aIf maternal karyotype is normal bIf parental karyotypes are normal an IC-deletion has to be determined as the recurrence risk is Network (EMQN) and the United Kingdom External 50% in case of a familial IC-deletion. Quality Assessment Scheme (UK NEQAS) for Molecular A summary of the causative genetic mechanisms and Genetics over a 5-year period. The guidelines were posted recurrence risks in PWS and AS is given in Tables 1 and 2. on the web-site of the UK Clinical Molecular Genetics There are a number of molecular genetic approaches to Society (CMGS; subsequently renamed The Association for confirm these two disorders. The most common is DNA- Clinical Genomic Science (ACGS) since 2016) for con- based methylation testing to detect hyper- or hypomethy- sultation and amendment between 19 May 2008 and 6 lation within the PWS and AS critical region. This will January 2010 and heads of the constituent laboratories were detect more than 99% of individuals with PWS and ~80% invited to comment. In the light of feedback amendments of individuals with AS. UBE3A sequence analysis detects were made and the final document was ratified by the disease causing variants in approximately a further 5–10% CMGS Executive Committee on 10 January 2010. In of individuals with AS, however UBE3A analysis is not addition they were approved by the European Molecular considered further in this article. Genetics Quality Network (EMQN) Steering Group on 22 January 2010. The updated version in this article was available through Methods the EMQN for consultation and amendment by the com- munity of 105 laboratories participating in the EMQN- The original guidelines for PWS and AS were assessed by organised scheme for PW/AS, between 20 June 2018 and consideration of the external quality assessment returns 13 July 2018. The feedback was collected, evaluated and submitted to the European Molecular Genetics Quality the draft document amended accordingly. Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1329

Results MLPA kit available from MRC Holland (http://www.mrc- holland.com). The MS-MLPA kit contains copy number Strategies for the analysis of PWS and AS probes, specific for sequences in or close to the PWS/AS critical region on 15q11q13 as well as outside the PWS/AS The approach to the laboratory diagnosis of PWS and AS region and on other chromosomes which serve as controls. depends on many factors, including the availability of Among the PWS/AS specific probes, there are methylation- samples, the arrangement of laboratory services and the sensitive probes that contain a HhaI restriction site. The patterns of referral. The most sensitive single approach to current MS-MLPA kit ME028-C1 contains five diagnosing PWS and AS is to study the methylation within methylation-sensitive probes from the PWS/AS region that 15q11q13 using molecular genetic techniques. These will represent differentially methylated sites (four for the detect deletions, UPD and ID by establishing either SNURF-SNRPN exon1/promoter region and intron 1 and hypermethylation/complete methylation (PWS) or hypo- one for MAGEL2), and another one from the completely methylation/complete absence of methylation (AS). Note unmethylated promoter region of UBE3A. Moreover, the kit that for AS mosaic cases only a partial hypomethylation is contains additional methylation-sensitive control probes for detected. Broadly speaking, methylation studies take one of completely unmethylated sequences from other chromo- two forms: somes that will indicate complete digestion by the HhaI enzyme and therefore serve as digestion control probes. (i) The simultaneous assessment of methylation status Dosage analysis by MS-MLPA offers the opportunity to and genomic dosage at numerous sites across the detect large deletions, the most frequent molecular lesions 15q11q13 region, by the use of methylation-sensitive in patients with PWS and AS. In rare cases, a larger deletion multiplex ligation-dependent probe amplification can extend telomeric. Another advantage of the MS-MLPA (MS-MLPA). This approach will confirm the diag- kit is that it will identify IC-deletions in PWS and AS cases nosis and further identify the presence of a causative with an ID. The kit ME028-C1 contains two probes for the deletion (large deletion or deletion of the imprinting SNRPN exon 1/promoter, a region which represents the centre (IC-deletion)). In the absence of a deletion smallest region of deletion overlap in patients with PWS methylation results alone are not sufficient to (PWS-SRO) and an IC-deletion. Furthermore, there are two discriminate between UPD and ID. Therefore, micro- probes for SNRPN exon U5 which can be used to detect IC- satellite analysis is required. deletions in patients with AS and an ID. Both lie in the (ii) The detection of methylation status solely at the smallest region of deletion overlap found in patients with SNRPN locus by use of methylation-specific PCR AS and an imprinting defect (AS-SRO). Beside IC-dele- (MS-PCR). This approach will confirm a diagnosis tions, small deletions affecting the SNORD116 gene region but will provide no further information regarding the or partly the UBE3A gene can be detected as well. For disease mechanism. Thus, it is still open whether the UBE3A deletion detection another MLPA kit (P336-B1, molecular cause is a large deletion, a UPD or an ID MRC Holland) is available that covers each exon. But this with or without an IC-deletion necessitating follow up is not the subject of these guidelines. studies (dosage analysis by MLPA or FISH, micro- MS-MLPA has become the method of choice in many satellite analysis, IC analysis (in case FISH was done diagnostic laboratories as it investigates methylation status for the deletion analysis)). of single CpGs at several positions inside a DMR, thereby reducing the risk of false-positive or false-negative results It is essential to note that approach (ii) will not distin- due to SNPs or technical problems. Whereas the MS-PCR is guish between the molecular causes. MS-MLPA however restricted to the CpGs at the primer binding site(s). provides more information in this regard (see below). Fig- There appears to be some naturally-occurring variation in ure 2 shows an example of testing strategies for approaches dosage and methylation status which must be taken into (i) and (ii). account when interpreting MS-MLPA results:

Molecular genetic testing methods (i) For the two most centromeric probes, NIPA1 and TUBGCP5, copy number variation has been observed. MS-MLPA This has been attributed to deletions and duplications encompassing these two probes, and complicates the MS-MLPA provides a means to simultaneously detect copy deﬁnition of class I and class II deletions. number changes and DNA methylation within 15q11q13 in The frequency of the BP1-BP2 duplication seems a semi-quantitative manner. Almost all laboratories using to be around 0.5% in the general population with the this approach make use of a commercially available MS- deletion being only slightly less frequent [23]. 1330 J. Beygo et al.

a MS-MLPA methylation analysis

50% methylation hypomethylation (AS) normal hypermethylation (PWS)

AS PWS deletion analysis no deletion microsatellite analysis highly unlikely

uniparental biparental

UBE3A imprinting defect heterozygous deletion upd(15) imprinting defect mutation analysis due to an IC-deletion 15q11q13 (~5-7 Mb) without underlying DNA change

deletion analysis chromosome analysis in the parents in index and parents*

familiar de novo recurrrence risk 50%

b MS-PCR methylation analysis

50% methylation hypomethylation (AS) normal hypermethylation (PWS)

AS PWS large deletion, upd(15) or ID highly unlikely

UBE3A further analyses needed mutation analysis e.g. dosage analysis, segregation analysis

Fig. 2 Testing strategies for the molecular analysis of PWS and AS cytogenetic rearrangements (e.g. Robertsonian translocations). In case using a MS-MLPA and b MS-PCR. Note that MS-PCR cannot dis- of PWS or AS due to a large, heterozygous deletion the father or the tinguish between the different molecular causes of AS and PWS. mother, respectively should be investigated *In case of a upd(15) both parents should be investigated to rule out

The phenotypic outcome of these copy number parents [27, 28]. Therefore, interpretation of these variations is still a matter of debate and especially the variants should be done with extreme caution. deletion has been linked to a wide variety of Variation in the hybridisation efﬁciency due to a phenotypic features from developmental delay to copy number variation is also observed for the congenital heart defects [24–26]. Newer studies point SNRPN exon u1B probe. to a (mild) effect in cognition, a low penetrance and a (ii) SNPs under hybridisation binding sites can inﬂuence high proportion of variants inherited from normal probe signals. Consequently, laboratories must exercise Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1331

extreme caution when interpreting results from a single techniques have not been widely adopted but have all been probe. used successfully within a diagnostic context. However, (iii) Normal variation in the degree of methylation at the like the MS-PCR, these alternative techniques only inves- MAGEL2 locus is frequently observed. tigate the methylation status and cannot distinguish between the different molecular causes. For prenatal diagnosis it should be noted that chorionic A SNP array analysis for PWS/AS testing is of limited villi and amniotic fluid samples show a significant hypo- suitability as it will identify only patients with a large deletion methylation at the MAGEL2 and NDN locus (Supplementary or an isodisomy for chromosomes 15. It will miss patients Fig. 1; ME028-C1 Description version C1–03; 24 January with heterodisomy 15 unless both parents are investigated by 2019, MRC Holland). These results suggest that the methy- SNP array as well and the genotypes are analysed in detail. Be lation of the MAGEL2 and NDN locus is not fully established aware that an ID cannot be detected by this technique. Fur- in chorionic tissue. It is therefore recommended that only the thermore, the parental origin of the deletion or the UPD (in methylation status of the SNRPN locusisconsideredinthe case parental samples have not been investigated) remains context of prenatal diagnosis. unknown. Consequently, patients who were found to have a It should be noted that the current commercially available deletion or an isodisomy and also patients without evidence MS-MLPA kit ME028 is not CE-IVD certified for diagnostic for a deletion must be investigated for methylation. use and must be fully validated in individual laboratories prior to implementation. We recommend that recurrent variation Microsatellite analysis (MSA) observed in the MRC MS-MLPA kit is reported to the manufacturer to facilitate future kit development. When a molecular diagnosis of AS or PWS is confirmed with any of the above techniques microsatellite analysis will MS-PCR often be required to distinguish between a UPD and an ID. In some cases MSA is also used to detect large deletions, if This is based on sodium bisulphite treatment of DNA fol- enough informative markers are present. However we lowed by PCR using primers specific for differentially would recommend dosage analysis by MLPA as this can methylated sites within the SNRPN exon 1/promoter immediately detect large and IC-deletions. regions. Two approaches have been shown to work reliably At present many microsatellites are available for chro- in interlaboratory comparisons: Kubota et al. [29] describe mosome 15, and it is outside the scope of this article to the use of two primer pairs that can be used separately provide a comprehensive list of suitable markers. However, (simplex PCR) or in combination (duplex PCR). However, it is worth noting the following markers that have been used it is strongly recommended that the primers are not used in a in the past and are known to be compromised: simplex reaction as this has been shown to result in spurious DNA amplification and/or misdiagnosis resulting from PCR ● D15S113. This is a CA repeat from within the critical failure [30]. Zeschnigk et al. [31] describe an alternative region. The presence of null alleles (or non- assay with one common primer that anneals to both alleles amplification alleles) has been observed with this marker and one specific primer each for the methylated and the and can complicate the analysis of AS and PWS cases. unmethylated allele. In this case, the three primers are Under certain conditions, a non-amplification allele can always used together in one reaction. The SNRPN exon 1/ be misinterpreted as a small deletion. The frequency of promoter region is highly conserved but contains some very these alleles in families without AS has been estimated rare single nucleotide polymorphisms (SNPs) within the to be around 4%. Alternative primers can be designed; primer binding sites (see Supplementary Fig. 2) that can however, this marker is best avoided. lead to false results. Such variants can now be found in ● D15S817. The presence of three alleles has been current open access databases [e.g. GnomAD http://gnoma observed with this marker with certain primer sets due d.broadinstitute.org/]. to complex duplications in the region where the marker Another point to consider is the challenging detection of is located. Since there is a low frequency/density of mosaic cases by MS-PCR. useful markers for the more centromeric PWS/AS region, the use of the following primer pair Alternative techniques (D15S817F,5′-TGGAACCAATAGGATAGACAC-3′ D15S817R,5′-GGTCAGCCTCCATAATCA-3′) can A small number of laboratories use alternative methods of resolve this problem. methylation analysis including PCR following restriction digestion with a methylation-sensitive enzyme [32], melt- For microsatellite analysis we recommend choosing curve analysis [33], and pyrosequencing [34]. These markers within and outside the PWS/AS region and 1332 J. Beygo et al. analysing an appropriate number of markers to be able to in the majority of patients with PWS and AS. In both make a solid interpretation. In some countries it is com- syndromes, the same region is affected, but in PWS the pulsory to analyse at least eight markers. Moreover, an deletion is always on the paternal chromosome, whereas in interpretation should never be built on one single informa- AS it is always on the maternal chromosome. This deletion tive marker. is probably one of the most common pathogenic deletions Once the diagnosis of PWS or AS has been confirmed observed in humans [7]. In a few patients, the region is using methylation analysis, the interpretation of the micro- deleted as the result of an unbalanced translocation. At the satellite results is as follows: molecular level, two classes of deletions (class I and II) can be distinguished. In both classes, the distal breakpoints are a. Uniparental inheritance both inside and outside the close to, but telomeric to the OCA2 gene (breakpoint region critical region: In this case, the disease is due to UPD. 3, BP3, see Fig. 1). In class I deletions (30–40% of deletion It is important to note that AS and PWS can be caused cases), the proximal breakpoint is centromeric to the marker by either chromosomal isodisomy or heterodisomy D15S541 (breakpoint region 1, BP1). In class II deletions (Meiosis I or Meiosis II non-disjunction). Further, (60–70% of deletion cases) the proximal breakpoint is heterodisomy or isodisomy at a single locus does not between D15S541 and D15S543 (breakpoint region 2, necessarily reflect the disomy status along the entire BP2). The clustering of the deletion breakpoints is due to chromosome depending on the rate and level of the presence of large duplicated sequence stretches of crossing over and the meiotic stage at which non- 200–400 kb in size in the common breakpoint regions that segregation occurred. are susceptible to non-homologous crossovers [39–41]. b. Biparental inheritance both inside and outside the There are rare cases with atypical deletions that can range critical region: In this case the disease is due to an ID. until BP4/BP5 [42]. Cases of large deletions should be Exclusion of an IC-deletion must ensue if not already further investigated by cytogenetic analysis to rule out the performed (e.g. by MS-MLPA). presence of (very rare) balanced cytogenetic rearrangements c. Uniparental inheritance inside the critical region, in the appropriate parent (father for PWS and mother for biparental outside: In this case the disease is most AS) that may predispose to a deletion. likely due to a deletion of the critical region. Laboratories must not interpret results from a single UPD informative microsatellite without supporting evidence. In very rare cases such a constellation can be The second most frequent finding in PWS is maternal UPD seen in patients with a segmental UPD [35]. (upd(15)mat; nomenclature according to ISCN 2016 [43]) of chromosome 15. These patients have two maternal copies of chromosome 15 and lack a paternal copy. As the pater- Interpretation of diagnostic testing results nally expressed genes are silent on the maternal chromosome, upd(15)mat is associated with a complete loss of Normal methylation result function of these genes. The reciprocal finding is made in 1–2% of patients with AS. These patients have two paternal A normal methylation pattern rules out PWS on the basis of copies of chromosome 15 and lack a maternal copy (upd most known cases to date (sensitivity ~99%) and around (15)pat). In brain cells UBE3A is silent on the paternal 80% of AS cases. chromosome, so upd(15)pat is associated with a complete Despite early reports of possible deletion mosaicism in loss of function of this gene in this tissue. UPD can arise as PWS [36, 37] the case for deletion mosaicism remains a result of meiotic and/or mitotic errors [44]. Mechanisms unproven [38]. include trisomy rescue, monosomy rescue, complementa- In the case of AS, if the clinical suspicion remains strong tion and postfertilisation error. During meiosis, the diploid with normal methylation then it is recommended to under- set of chromosomes (n = 46) is reduced to a haploid set take UBE3A analysis as mutations in this gene will have a (n = 23). Nondisjunction of the homologous chromosomes recurrence risk of 50% if the mother is a non-mosaic 15 during, e.g., female meiosis I or nondisjunction of the mutation carrier. two sister chromatids during female meiosis II results in an oocyte with two chromosomes 15 or no chromosome 15. In Deletions these cases, fertilisation by a sperm with one chromosome 15 will result in a zygote which is trisomic or monosomic The de novo interstitial deletion of chromosome 15, del(15) for chromosome 15 respectively. These conditions are not (q11q13), which includes the entire imprinted domain plus compatible with normal development, but can be ‘rescued’ several non-imprinted genes, extends ~5–7 Mb and is found by loss of one chromosome 15 from a trisomic cell or Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1333 duplication of the paternal chromosome 15 in a monosomic occurred after fertilisation and is not associated with an cell. With trisomy rescue, in two-thirds of cases, one of the increased recurrence risk [15]. two maternal chromosomes will be lost from the trisomic cell, resulting in a normal set of chromosomes. If, however, Reporting the paternal chromosome is lost, the cell is left with two maternal chromosomes 15 (upd(15)mat; PWS). Duplication Some general considerations for the reports: of the paternal chromosome 15 in a monosomic cell will lead to upd(15)pat (AS). ● It is recommended that laboratories do not use joint Alternative mechanisms for UPD such as com- PWS/AS report templates. plementation involving both a nullisomic and disomic ● It is essential to state clearly on the report the method(s) gamete or rescued paternal 15 trisomy have also been used to carry out genetic analysis, with an appropriate reported, however are considered rare [45]. reference; for example, “ME028-C1 (MRC Holland)”, Cases of UPD should be further investigated by cyto- always including the version number or “Zeschnigk genetic analysis to rule out the presence of a (very rare) et al. 1997 Eur J Hum Genet, 5:94-99”. balanced Robertsonian translocation in one of the parents - ● Identifier of the patient and of all other family members both parents have to be analysed irrespective of a detected from whom a sample was used for diagnostics, e.g. in upd(15)mat or upd(15)pat. MSA, must be given. ● The source of the DNA sample should be given on the Imprinting defects report, as it can be important for example in case of prenatal diagnosis. There are a small number of patients with either PWS ● Results should be reported in a clear and concise (1%) or AS (3%) that show a hypermethylation/complete fashion. The interpretation should be given separately methylation or hypomethylation/complete absence of and not be merged with the results. methylation, respectively, without a large deletion of ● It should be stated clearly that ‘the diagnosis of PWS or 15q11q13. Moreover, they show biparental inheritance for AS is confirmed’. Phrasings like ‘is consistent with’, chromosome 15 markers, both inside and outside the ‘supports the diagnosis’, ‘is in accordance with’, ‘are critical region. These patients have an ID. The majority of compatible with’ are ambiguous. these patients are sporadic cases without any detectable ● Reports should inform about the recurrence risk. deletion or a DNA sequence change at the IC region. ● Genetic counselling should be offered to all families However, in 10–15% of cases, the ID is caused by an IC- irrespective of whether a diagnosis is confirmed or not deletion. In most cases, the IC-deletion is familial and (different standards may apply in different countries). thus associated with a 50% recurrence risk. In some cases ● Limitations and test sensitivity should be mentioned if the IC-deletion is de novo or a consequence of germ line diagnosis could not be confirmed (e.g. low grade mosaicism in the father or the mother. In these families, mosaicism might escape detection). the recurrence risk ranges from 0–50%, depending on the ● Inadequate terms to describe methylation results should degree of the mosaicism in the germ line [16]. An IC- be avoided. For the description of the result obtained deletion is the only kind of DNA sequence change found terms as ‘PWS pattern’, ‘abnormal methylation pattern’, in patients with an ID with the exception of a single case ‘change in methylation’ or ‘pathological result’ are not where a familial inversion has been identified which dis- appropriate. The best is to describe what is observed. rupts the IC region [46]. Examples for such descriptions including adequate If a laboratory does not use an assay capable of assessing terms of the methylation result are given below. copy number in the AS- and PWS-SROs then, in the case of a confirmed diagnosis where a common deletion or UPD More specific recommendations are as follows: has been excluded, it is essential that the family workup is completed in a laboratory able to undertake this test. On Diagnostic referral for PWS (MS-MLPA) confirmation of an IC-deletion parents should also be tested if available (father in case of PWS and mother in case of AS) to establish recurrence risks in the family. (i) Normal methylation and normal gene dosage at As mentioned before, more than 40% of AS imprinting 15q11q13 detected: defect patients without an IC-deletion have a partial hypo- This result excludes a large deletion on the paternal methylation and therefore are somatic mosaics for an ID allele, a UPD of chromosome 15 and an ID. A (the detected degree of hypomethylation depends on the diagnosis of PWS is highly unlikely (sensitivity of the number of cells carrying the ID). In these cases the ID test ~99%). 1334 J. Beygo et al.

(ii) Heterozygous deletion and hypermethylation/com- If appropriate other family members should be plete methylation detected: investigated, too. Gene dosage analysis shows a 50% reduction for # probes within the chromosomal region 15q11q13 (33 Diagnostic referral for PWS (using MS-PCR or a of probes from TUBGCP5 to OCA2, class I deletion; comparable alternative technique) 31 of probes from MKRN3 to OCA2, class II deletion; number of probes depending on the kit version used, here ME028-C1). The methylation analysis shows a (i) Normal methylation at 15q11q13 detected: hypermethylation/complete methylation at all five This result excludes a large deletion on the paternal methylation-sensitive probes, indicating that the 15q11q13 allele, a UPD of chromosome 15 and an ID. deletion is on the paternal allele. A diagnosis of PWS is highly unlikely (sensitivity of This result confirms the diagnosis of PWS. The the test ~99%). molecular cause is a heterozygous deletion within (ii) Hypermethylation/complete methylation detected: 15q11q13 (class I or class II deletion) on the paternal No paternal, unmethylated band detected in the allele. methylation analysis at 15q11q13. This result confirms Cytogenetic analysis in the patient and the father the diagnosis of PWS. The underlying molecular cause should be performed to rule out the presence of can be either a large deletion of 15q11q13 on the cytogenetic rearrangements which would increase the paternal allele, a maternal UPD of chromosome 15 or recurrence risk. an ID (with or without an IC-deletion). Further (iii) Normal gene dosage and hypermethylation/complete molecular genetic testing (e.g. dosage analysis) is methylation detected: necessary. Normal gene dosage, but a hypermethylation/ As MS-PCR or equivalent methods that investigate complete methylation at all five methylation-specific only the methylation status cannot differentiate between probes. This result confirms the diagnosis of PWS. the possible molecular genetic mechanisms underlying The molecular cause of PWS is either a maternal UPD the PWS diagnosis, additional investigations regarding of chromosome 15 or an ID. gene dosage and segregation of chromosome 15 have to Microsatellite analysis should be performed in the be requested. This is of utmost importance as the family to differentiate between a upd(15)mat recurrence risk cannot be determined without knowl- and an ID. edge of the underlying molecular genetic cause. If a upd(15)mat is confirmed subsequent cytogenetic analyses should be performed in the patient and the parents to rule out cytogenetic rearrangements Diagnostic referral for AS (MS-MLPA) which would increase the recurrence risk. If an ID is confirmed the recurrence risk is not increased, since an IC-deletion has been excluded. (i) Normal methylation and normal gene dosage at (iv) Heterozygous deletion of the IC and hypermethyla- 15q11q13 detected: tion/complete methylation detected: This result excludes a large deletion on the Gene dosage analysis shows a 50% reduction for # maternal allele, a UPD of chromosome 15 and an ID. probes located in the IC (number and names of probes This result does not exclude a diagnosis of AS. according to the kit version used). The methylation Analysis of UBE3A should ensue if the clinical re- analysis shows a hypermethylation/complete methyla- assessment of the patient still suggests AS. tion at all five methylation-specific probes, indicating (ii) Heterozygous deletion and hypomethylation/complete that the IC-deletion is on the paternal allele. absence of methylation detected: This result confirms the diagnosis of PWS. The Gene dosage analysis shows a 50% reduction for # molecular cause of PWS is an ID due to an IC-deletion. probes within the chromosomal region 15q11q13 (33 MS-MLPA analysis in the father should be recom- of probes from TUBGCP5 to OCA2, class I; 31 of mended to estimate the recurrence risk. If the father is a probes from MKRN3 to OCA2, class II; number of non-mosaic carrier of the IC-deletion the recurrence risk probes depending on the kit version used, here is 50%. If he has no detectable deletion in blood DNA ME028-C1). The methylation analysis shows a this does not exclude germ line mosaicism, which is hypomethylation/complete absence of methylation at also associated with an increased recurrence risk (see all five methylation-specific probes, indicating that the section “Imprinting defect”). deletion is on the maternal allele. Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1335

This result confirms the diagnosis of AS. The mosaicism which is associated with an increased molecular cause is a heterozygous deletion within recurrence risk (see section “Imprinting defect”). 15q11q13 (class I or class II deletion) on the maternal allele. If appropriate other family members should be Cytogenetic analysis in the patient and the mother investigated, too. should be performed to rule out the presence of cytogenetic rearrangements which would increase the Diagnostic referral for AS (using either MS-PCR or a recurrence risk. comparable alternative technique) (iii) Normal gene dosage and hypomethylation/complete absence of methylation detected: Normal gene dosage, but a hypomethylation/ (i) Normal methylation at 15q11q13 detected: complete absence of methylation at all five This result excludes a large deletion on the methylation-specific probes. This result confirms the maternal allele, a UPD of chromosome 15 and an ID. diagnosis of AS. The molecular cause of AS is either a This result does not exclude a diagnosis of AS. paternal UPD of chromosome 15 or an ID. Analysis of UBE3A should be performed if the Microsatellite analysis should be performed in the clinical re-assessment of the patient still suggests AS. family to differentiate between a upd(15)pat (ii) Hypomethylation/complete absence of methylation and an ID. detected: If a upd(15)pat is confirmed subsequent cytoge- No maternal, methylated band detected in the netic analyses should be performed in the patient and methylation analysis at 15q11q13. This result con- the parents to rule out cytogenetic rearrangements firms the diagnosis of AS. The underlying molecular which would increase the recurrence risk. cause can be either a large deletion of 15q11q13 on If an ID is confirmed the recurrence risk is not the maternal allele, a paternal UPD of chromosome 15 increased, since an IC-deletion has been excluded. or an ID with or without an IC-deletion. Further (iv) Normal gene dosage and partial hypomethylation/ molecular genetic testing (e.g. dosage analysis) is partial absence of methylation detected: necessary. Normal gene dosage, but a partial hypomethyla- (iii) Partial hypomethylation/partial absence of methylation/partial absence of methylation at all five tion detected: methylation-specific probes. This result confirms the A faint maternal, methylated band detected in the diagnosis of AS. The partial hypomethylation/partial methylation analysis at 15q11q13. This result con- absence of methylation indicates that a somatic firms the diagnosis of AS. The underlying molecular mosaic is present where cells with a normal imprint cause can be either a large deletion of 15q11q13 on and cells with either a paternal UPD of chromosome the maternal allele, a paternal UPD of chromosome 15 15 or an ID are present. or an ID each in a mosaic state. Most likely are a UPD Microsatellite analysis should be performed in the and an ID. Further molecular genetic testing (e.g. family to differentiate between these two possibilities. microsatellite analysis) is necessary. (v) Heterozygous deletion of the IC and hypomethylation/ complete absence of methylation detected: As MS-PCR or equivalent methods that investigate only Gene dosage analysis shows a 50% reduction for # the methylation status cannot differentiate between the probes located in the IC (number and names of probes possible molecular genetic mechanisms underlying the AS according to the kit version used). The methylation diagnosis, additional investigations regarding gene dosage analysis shows a hypomethylation/complete absence and segregation of chromosome 15 have to be requested. of methylation at all five methylation-specific probes, This is of utmost importance as the recurrence risk cannot indicating that the IC-deletion is on the maternal be determined without knowledge of the underlying mole- allele. cular genetic cause. This result confirms the diagnosis of AS. The molecular cause of AS is an ID due to an IC- Prenatal diagnosis deletion. MS-MLPA analysis in the mother should be When the diagnosis has been confirmed and the molecular performed to estimate the recurrence risk. If the cause has been established in the index patient, prenatal mother is a non-mosaic carrier of the IC-deletion diagnosis can be offered to the family. In case of a de novo the recurrence risk is 50%. However, an absence of deletion or UPD the recurrence risk is very low given that the deletion in blood does not exclude a germ line the parental chromosomes are normal. Recurrence risk for 1336 J. Beygo et al.

IDs without an IC-deletion is low. However, prenatal testing patients with Schaaf-Yang syndrome (#615547). The phe- can be offered to the families for reassurance regardless of notypic overlap with PWS includes neonatal hypotonia, the underlying molecular cause. For cases of familial intellectual disability and later onset of obesity. Con- deletions of the IC prenatal diagnosis should be offered as tractures of interphalangeal joints can serve as a distin- the recurrence risk is high (50%). Methylation status at guishing feature [54, 55]. Only disease causing variants on SNRPN exon 1 is established early in embryonic develop- the paternal allele are causative so that a silent transmission ment and testing DNA extracted from both amniotic cells over several generations is possible. Deletions of the whole and chorionic villi (both native and cultured) has been gene have been reported, but do not lead to PWS or a shown to give reliable results [47]. The methylation at the similar phenotype [56, 57]. NDN locus should not be interpreted in case of prenatal testing. The methylation at the MAGEL2 locus is more Angelman syndrome similar to the methylation status at the SNRPN region than NDN, but may not always be fully established at time of Around 10–15% of patients with a clinical diagnosis of AS sampling, and is therefore not reliable and should also not have no detectable disturbance at 15q11q13 using the be interpreted in case of prenatal testing (ME028-C1 techniques described here. In rare cases, these patients may Description version C1-03; 24 January 2019, MRC Hol- be low grade mosaics for an imprinting defect. However, it land; Supplementary Fig. 1). is more likely that there is an alternative clinical diagnosis For cases of ID due to IC-deletions or disease causing and a careful review of the patient’s history, clinical features variants in UBE3A in AS cases that are either de novo or a and EEG findings is recommended. One diagnosis which consequence of germ line mosaicism in the parent, the should be considered in girls is Rett syndrome caused by recurrence risk is difficult to predict but may be as high as haploinsufficiency of the MECP2 gene located on chro- 50%. In cases of sporadic ID with no detectable deletion, mosome Xq (male Rett syndrome is rare but possible) the recurrence risk appears to be low, however since the [58, 59]. It is extremely difficult to distinguish between Rett possibility of recurrence cannot be excluded a prenatal syndrome and AS during infancy when both can present diagnosis should be offered. with acquired microcephaly, ataxia and frequent smiling. Later, Rett syndrome may be distinguished by the presence Differential diagnoses of a history of developmental regression, the emergence of stereotypic hand-wringing movements, bouts of hyperven- Prader-Willi syndrome tilation and the presence of vasomotor disturbance. If there is a very early onset of seizures, within the first few months, Diagnoses which need to be considered in infants with disease causing variants within the CDKL5 gene should be hypotonia include congenital myopathies, central and per- considered [60]. Mowat-Wilson syndrome, caused by dis- ipheral neuromuscular disorders, especially type 1 spinal ease causing variants in the ZEB2 gene on chromosome 2q, muscular atrophy and the congenital form of myotonic is associated with severe learning disability, limited speech, dystrophy. Furthermore anomalies of the central nervous seizures and characteristic facial features that resemble system and peroxisomal disorders should also be ruled out those of AS. In addition Hirschsprung disease, congenital if chromosome 15 methylation is normal [7, 48]. cardiac defects and agenesis of the corpus callosum may be A further phenotype which presents with neonatal associated with disease causing variants in ZEB2. A strong hypotonia and short stature together with later-onset obesity indication is the characteristic appearance of the ear lobes is Temple syndrome, an imprinting disorder which can be which are upturned and look like “shell pasta”. Pitt-Hopkins caused by deletions, ID and upd(14)mat involving the Syndrome (PHS) is a sporadic condition caused by disease chromosomal region 14q32 [49, 50]. causing variants or deletions of the TCF4 gene on chro- When considering the differential diagnosis of older mosome 18q. Patients present with absent speech, seizures children with learning disability and obesity, Cohen syn- and facial features resembling AS, together with a sociable drome, Borjesson-Forssman-Lehman syndrome (males), personality. The facial appearance in PHS coarsens with age Bardet-Biedl syndrome, Alstrom syndrome and Fragile X and the lips in particular become prominent. Episodes of syndrome along with chromosomal disorders including hyperventilation and apnoea may develop [61, 62]. Auto- diploid/triploid mosaicism, 1p36 microdeletion syndrome somal recessive forms of PHS (Pitt-Hopkins-like syndrome and 16p11.2 deletion syndrome, should be considered [51]. 1 and 2) are caused by deletions and disease causing var- In many of these cases the facial phenotype differs from iants in the genes CNTNAP2 and NRXN1. Breathing PWS [52, 53]. anomalies, epilepsy and autistic features are prominent Truncating disease causing variants of the imprinted features in these cases [63, 64]. Another Angelman-like MAGEL2 gene on 15q11q13 have been described in condition is the X-linked Christianson syndrome caused by Update of the EMQN/ACGS best practice guidelines for molecular analysis of Prader-Willi and Angelman. . . 1337 disease causing variants in the SLC9A6 gene [65, 66]. International Laboratory Accreditation Cooperation (ILAC) Specific characteristics to look for in this condition are eye or equivalent national accreditation body. movement abnormalities, a slim body habitus and an unu- All tests should be validated/verified in individual sually fast EEG rhythm. Furthermore, haploinsufficiency of laboratories prior to implementation; it is not acceptable to the MEF2C gene has been described due to larger deletions rely on the validation of a test by another laboratory, since as well as disease causing variants in patients with intel- that does not guarantee that it will perform accurately and lectual disability, absence of speech and seizures. Addi- reliably in all labs. A series of control samples representing tionally, stereotypic movements were present [67, 68]. all disease causing variant types should therefore be col- Several chromosome abnormalities have phenotypes that lected by each laboratory to facilitate test validation/ver- overlap with AS. The most common are the ification, and exchange of samples between laboratories is 1p36 subtelomeric deletion, a microdeletion of 17q21, and a encouraged to allow this. External quality assessment terminal deletion of 22q13 [69, 70]. Xq28 duplication (EQA) schemes provide further validation of testing pro- including the MECP2 gene may also present with a phe- cedures and methods, and laboratories should participate notype suggestive of AS in males [71]. Profound neonatal annually in appropriate EQA schemes for PWS and AS hypotonia, the presence of constipation and Rett-like fea- testing. If this is not possible, inter-laboratory exchange of tures distinguish Xq28 duplication from AS patients [72]. samples should be arranged to compare and validate test Several patients with 2q23.1 microdeletions encompassing results. the methyl binding domain gene MBD5 and a clinical and behavioural phenotype reminiscent of AS were reported [73]. Seizures, ataxia and sleep disturbance were common Discussion/conclusion findings in this group of patients. Microarray studies are therefore clearly indicated in patients with AS-like features. This is an update of the practical set of molecular genetic Some rare metabolic disorders may present with AS-like testing and reporting guidelines that have been developed symptoms. Methyltetrahydrofolate reductase (MTHFR) for PWS and AS by Ramsden and colleagues [1]. The deficiency and adenylosuccinate lyase deficiency have been update takes into account new developments in terms of reported as presenting with learning disability, ataxia, sei- techniques, differential diagnoses and reporting standards. zures, autistic features and excessive laughter [74, 75]. With Feedback has been obtained from participants of the MTHFR deficiency homocystinuria is present and treatment 2018 PWS/AS EMQN external quality assessment scheme with folic acid and betaine may alleviate, though not (105 laboratories from 29 countries). Nine comments were completely cure symptoms. received; most were minor largely typographic corrections Haploinsufficiency of HERC2, ATRX, FOXG1, STBPX1 and some points of clarity. There was no disagreement on and SYNGAP1 show some overlapping phenotypic features the recommendations made. All comments have been with AS [70, 76, 77]. incorporated into this final document. Lastly, AS patients with mosaic ID can lack the typical features like absence of speech, ataxia and happy demea- Acknowledgements This work has been adapted from the original “ nour but can instead present with features typical for PWS article Practice Guidelines for Molecular Analysis of Prader-Willi and Angelman Syndromes” by Ramsden SC, Clayton-Smith J, Birch R, like hypotonia, obesity and developmental delay [78]. Buiting K 2010, BMC Med Genet 2010; 11:70. (https://doi.org/10. 1186/1471-2350-11-70; https://bmcmedgenet.biomedcentral.com/a Internal and external quality control rticles/10.1186/1471-2350-11-70). The original article is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), The EMQN recommends that all laboratories offering which permits unrestricted use, distribution, and reproduction in any molecular genetic testing for PWS and AS must follow medium, provided the original work is properly cited. Part of this work established good laboratory practice, as documented for was funded by the Bundesministerium für Bildung und Forschung example in Guidelines for Quality Assurance in Molecular (BMBF, Network Imprinting diseases, Grant No. 01GM1513A). The guideline update process was supported and facilitated by the EMQN Genetic Testing, published by the Organisation for Eco- team in Manchester, UK. nomic Co-operation and Development [79]. In addition to following such guidelines, a laboratory Compliance with ethical standards should ideally demonstrate that it complies with inter- nationally recognised standards for laboratory testing (e.g. Conflict of interest The authors declare that they have no conflict of ISO standards 15189: 2012 Medical laboratories interest. –requirements for quality and competence), by achieving Publisher’s note: Springer Nature remains neutral with regard to formal accreditation with a member organisation of the jurisdictional claims in published maps and institutional affiliations. 1338 J. Beygo et al.

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