Macrocephaly / Overgrowth Syndrome Panel

Last modified: Jun 12, 2018

Summary

  • Is a 43 gene panel that includes assessment of non-coding variants
  • Is ideal for patients with a clinical suspicion of syndromes resulting in early overgrowth or macrocephaly.

Analysis methods

  • PLUS
  • SEQ
  • DEL/DUP

Availability

4 weeks

Number of genes

43

Test code

MA1401

Panel size

Large

CPT codes

SEQ 81403
SEQ 81405
SEQ 81406
DEL/DUP 81479

Summary

The Blueprint Genetics Macrocephaly / Overgrowth Syndrome Panel (test code MA1401):

  • Is a 43 gene panel that includes assessment of selected non-coding disease-causing variants
  • Is available as PLUS analysis (sequencing analysis and deletion/duplication analysis), sequencing analysis only or deletion/duplication analysis only

ICD codes

Commonly used ICD-10 code(s) when ordering the Macrocephaly / Overgrowth Syndrome Panel

ICD-10 Disease
Q75.3 Macrocephaly
Q87.3 Congenital malformation syndromes involving early overgrowth

Sample Requirements

  • EDTA blood, min. 1 ml
  • Purified DNA, min. 3μg
  • Saliva (Oragene DNA OG-500 kit)

Label the sample tube with your patient’s name, date of birth and the date of sample collection.

Note that we do not accept DNA samples isolated from formalin-fixed paraffin-embedded (FFPE) tissue.

Macrocephaly is a condition in which the head is abnormally large (circumference > +2.5 SD of normal for weight and gender). Many people with an unusually large head and large skull are healthy, however macrocephaly is also a feature of several syndromes. Macrocephaly may be due to megalencephaly (true enlargement of the brain) or due to other conditions such as hydrocephalus or cranial thickening and is a common reason for referral to the genetics clinic. Macrocephaly is associated with many genetic disorders and this panel can be used for their differential diagnostics. Syndromic and nonsyndromic forms of pathologic macrocephaly may be caused by congenital anatomic abnormalities or genetic conditions, but the disease may also be nongenetic and caused by environmental events. The genetic macrocephaly conditions cover a broad spectrum of gene disorders and their related proteins have diverse biological functions. As of yet it is not clear what precise biological pathways lead to generalized brain overgrowth, but several genes have been identified. Genetic types of macrocephaly include: 1) familial macrocephaly (benign asymptomatic), 2) autism disorder (multifactorial, non-syndromic type), 3) syndrome associations (multiple types) 3A) with cutaneous findings (PTEN hamartoma syndromes, neurofibromatosis, type 1 hemimegalencephaly), 3B) with overgrowth (Sotos, Weaver, Macrocephaly-Cutis Marmorata Telangiectasia Congenita, Simpson-Golabi-Behmel, Beckwith-Wiedemann Syndrome), 3C) neuro-cardio-facial-cutaneous syndromes (Noonan, Costello, Cardiofaciocutaneous, LEOPARD) with intellectual disability (Fragile X syndromes), 4) metabolic types with leukodystrophy (Alexander, Canavan, megalencephalic leukodystrophy, organic acidurias, glutaric aciduria, type 1, D-2-hydroxyglutaric aciduria) and 5) hydrocephalus (aqueductal stenosis types and multifactorial, non-obstructive types).

Genes in the Macrocephaly / Overgrowth Syndrome Panel and their clinical significance

Gene Associated phenotypes Inheritance ClinVar HGMD
AKT1 Proteus syndrome, Cowden syndrome AD 5 6
AKT3 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome AD 12 27
ASPA Aspartoacylase deficiency (Canavan disease) AR 39 102
BRWD3 Mental retardation XL 9 16
CCND2 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome AD 8 8
CDKN1C Beckwith-Wiedemann syndrome, IMAGE syndrome AD 28 81
CHD8 Autism AD 36 59
CUL4B Mental retardation, syndromic, Cabezas XL 23 37
DHCR24 Desmosterolosis AR 6 8
DIS3L2* Perlman syndrome AR 10 11
DNMT3A Tatton-Brown-Rahman syndrome AD 34 45
EED Cohen-Gibson syndrome AD 4 6
EIF2B5 Leukoencephalopathy with vanishing white matter, Ovarioleukodystrophy AR 21 96
EZH2 Weaver syndrome AD 29 40
GFAP Alexander disease AD 114 131
GLI3 Acrocallosal syndrome, Pallister-Hall syndrome, Grieg cephalopolysndactyly syndrome, Postaxial polydactyly type A, Preaxial polydactyly type 3, Preaxial polydactyly type 4 AD 63 229
GPC3 Simpson-Golabi-Behmel syndrome XL 29 72
GPSM2 Deafness, Chudley-McCullough syndrome AR 17 11
GRIA3 Mental retardation XL 12 21
HEPACAM Megalencephalic leukoencephalopathy with subcortical cysts, remitting AD/AR 12 26
HUWE1 Mental retardation, syndromic, Turner XL 37 37
KIAA0196 Spastic paraplegia, Ritscher-Schinzel syndrome (3C syndrome) AD/AR 10 16
KIF7 Acrocallosal syndrome, Hydrolethalus syndrome, Al-Gazali-Bakalinova syndrome, Joubert syndrome AR/Digenic 23 40
KPTN Mental retardation, autosomal recessive 41 AR 5 5
L1CAM Mental retardation, aphasia, shuffling gait, and adducted thumbs (MASA) syndrome, Hydrocephalus due to congenital stenosis of aqueduct of Sylvius, Spastic, CRASH syndrome, Corpus callosum, partial agenesis XL 71 287
MED12 Ohdo syndrome, Mental retardation, with Marfanoid habitus, FG syndrome, Opitz-Kaveggia syndrome, Lujan-Fryns syndrome XL 29 27
MLC1 Megalencephalic leukoencephalopathy with subcortical cysts AR 30 108
MPDZ Hydrocephalus, nonsyndromic, autosomal recessive 2 AR 9 22
NFIX Marshall-Smithsyndrome AD 43 65
NSD1 Sotos syndrome, Weaver syndrome, Beckwith-Wiedemann syndrome AD 303 515
OFD1 Simpson-Golabi-Behmel syndrome, Retinitis pigmentosa, Orofaciodigital syndrome, Joubert syndrome XL 142 157
PIGA* Multiple congenital anomalies-hypotonia-seizures syndrome XL 24 24
PIK3CA* Cowden syndrome, CLOVES AD 86 53
PIK3R2 Megalencephaly-polymicrogyria-polydactyly-hydrocephalus syndrome 1 AD 8 7
PTCH1 Basal cell nevus syndrome AD 147 411
PTEN* Bannayan-Riley-Ruvalcaba syndrome, Lhermitte-Duclos syndrome, Cowden syndrome AD 398 627
RAB39B Waisman parkinsonism-mental retardation syndrome, Mental retardation XL 6 17
RNF135 Macrocephaly, macrosomia, facial dysmorphism syndrome AD 6 6
SETD2 Luscan-Lumish syndrome AD 10 14
SYN1 Epilepsy, with variable learning disabilities and behavior disorders XL 11 7
TSC1 Lymphangioleiomyomatosis, Tuberous sclerosis AD 138 346
TSC2 Lymphangioleiomyomatosis, Tuberous sclerosis AD 322 1137
UPF3B Mental retardation, syndromic XL 9 18

* Some, or all, of the gene is duplicated in the genome. Read more.

# The gene has suboptimal coverage (means <90% of the gene’s target nucleotides are covered at >20x with mapping quality score (MQ>20) reads).

The sensitivity to detect variants may be limited in genes marked with an asterisk (*) or number sign (#)

Gene refers to the HGNC approved gene symbol; Inheritance refers to inheritance patterns such as autosomal dominant (AD), autosomal recessive (AR), X-linked (XL), X-linked dominant (XLD) and X-linked recessive (XLR); ClinVar refers to the number of variants in the gene classified as pathogenic or likely pathogenic in this database (ClinVar); HGMD refers to the number of variants with possible disease association in the gene listed in Human Gene Mutation Database (HGMD). The list of associated, gene specific phenotypes are generated from CGD or Orphanet databases.

Non-coding variants covered by the panel

Gene Genomic location HG19 HGVS RefSeq RS-number
CDKN1C Chr11:2905209 c.*5+20G>T NM_000076.2 rs760540648
EIF2B5 Chr3:183855941 c.685-13C>G NM_003907.2
L1CAM ChrX:153133652 c.1704-75G>T NM_000425.4
L1CAM ChrX:153131293 c.2432-19A>C NM_000425.4
L1CAM ChrX:153128846 c.3531-12G>A NM_000425.4
L1CAM ChrX:153136500 c.523+12C>T NM_000425.4
OFD1 ChrX:13773245 c.1130-22_1130-19delAATT NM_003611.2 rs312262865
OFD1 ChrX:13768358 c.935+706A>G NM_003611.2 rs730880283
PTCH1 Chr9:98226337 c.2561-2057A>G NM_000264.3
PTEN Chr10:89623226 c.-1001T>C NM_000314.4
PTEN Chr10:89623116 c.-1111A>G NM_000314.6
PTEN Chr10:89623056 c.-1171C>T NM_000314.6 rs587779981
PTEN Chr10:89623049 c.-1178C>T NM_000314.6
PTEN Chr10:89622988 c.-1239A>G NM_000314.6
PTEN Chr10:89623462 c.-765G>A NM_000314.4
PTEN Chr10:89623373 c.-854C>G NM_000314.4
PTEN Chr10:89623365 c.-862G>T NM_000314.4 rs587776675
PTEN Chr10:89622883–89623482
PTEN Chr10:89623331 c.-896T>C NM_000314.4
PTEN Chr10:89623306 c.-921G>T NM_000314.4
PTEN Chr10:89623296 c.-931G>A NM_000314.4 rs587781959
PTEN Chr10:89692749 c.254-21G>C NM_000314.4
TSC2 Chr16:2098067 c.-30+1G>C NM_000548.3 rs587778004
TSC2 Chr16:2127477 c.2838-122G>A NM_000548.3
TSC2 Chr16:2138031 c.5069-18A>G NM_000548.3 rs45484794
TSC2 Chr16:2110656 c.976-15G>A NM_000548.3 rs45517150

Added and removed genes from the panel

Genes added Genes removed
EED
KPTN
MPDZ
PIK3R2
RNF135
SETD2
ABCC6

Test strength

The strengths of this test include:
  • CAP and ISO-15189 accreditations covering all operations at Blueprint Genetics including all Whole Exome Sequencing, NGS panels and confirmatory testing
  • CLIA-certified personnel performing clinical testing in a CLIA-certified laboratory
  • Powerful sequencing technologies, advanced target enrichment methods and precision bioinformatics pipelines ensure superior analytical performance
  • Careful construction of clinically effective and scientifically justified gene panels
  • Our Nucleus online portal providing transparent and easy access to quality and performance data at the patient level
  • Our publically available analytic validation demonstrating complete details of test performance
  • ~1,500 non-coding disease causing variants in Blueprint WES assay (please see below ‘Non-coding disease causing variants covered by this panel’)
  • Our rigorous variant classification based on modified ACMG variant classification scheme
  • Our systematic clinical interpretation workflow using proprietary software enabling accurate and traceable processing of NGS data
  • Our comprehensive clinical statements

Test limitations

Genes with partial, or whole gene, segmental duplications in the human genome are marked with an asterisk (*) if they overlap with the UCSC pseudogene regions. The technology may have limited sensitivity to detect variants in genes marked with these symbols (please see the Panel content table above).

This test does not detect the following:
  • Complex inversions
  • Gene conversions
  • Balanced translocations
  • Mitochondrial DNA variants
  • Repeat expansion disorders unless specifically mentioned
  • Non-coding variants deeper than ±20 base pairs from exon-intron boundary unless otherwise indicated (please see above Panel Content / non-coding variants covered by the panel).

This test may not reliably detect the following:

  • Low level mosaicism (variant with a minor allele fraction of 14.6% is detected with 90% probability)
  • Stretches of mononucleotide repeats
  • Indels larger than 50bp
  • Single exon deletions or duplications
  • Variants within pseudogene regions/duplicated segments

The sensitivity of this test may be reduced if DNA is extracted by a laboratory other than Blueprint Genetics.

For additional information, please refer to the Test performance section and see our Analytic Validation.

The Blueprint Genetics macrocephaly / overgrowth syndrome panel covers classical genes associated with macrocephaly and Congenital malformation syndromes involving early overgrowth. The genes on the panel have been carefully selected based on scientific literature, mutation databases and our experience.

Our panels are sliced from our high-quality whole exome sequencing data. Please see our sequencing and detection performance table for different types of alterations at the whole exome level (Table).

Assays have been validated for different starting materials including EDTA-blood, isolated DNA (no FFPE), saliva and dry blood spots (filter card) and all provide high-quality results. The diagnostic yield varies substantially depending on the assay used, referring healthcare professional, hospital and country. Blueprint Genetics' Plus Analysis (Seq+Del/Dup) maximizes the chance to find a molecular genetic diagnosis for your patient although Sequence Analysis or Del/Dup Analysis may be a cost-effective first line test if your patient's phenotype is suggestive of a specific mutation type.

Performance of Blueprint Genetics Whole Exome Sequencing (WES) assay. All individual panels are sliced from WES data.

Sensitivity % (TP/(TP+FN) Specificity %
Single nucleotide variants 99.65% (412,456/413,893) >99.99%
Insertions, deletions and indels by sequence analysis
1-10 bps 96.94% (17,070/17,608) >99.99%
11-50 bps 99.07% (957/966) >99.99%
Copy number variants (exon level dels/dups)
Clinical samples (small CNVs, n=52)
1 exon level deletion 92.3% (24/26) NA
2 exons level deletion/duplication 100.0% (11/11) NA
3-7 exons level deletion/duplication 93.3% (14/15) NA
Microdeletion/-duplication sdrs (large CNVs, n=37))
Size range (0.1-47 Mb) 100% (37/37)
Simulated CNV detection
2 exons level deletion/duplication 90.98% (7,357/8,086) 99.96%
5 exons level deletion/duplication 98.63% (7,975/8,086) 99.98%
     
The performance presented above reached by WES with the following coverage metrics
     
Mean sequencing depth at exome level 174x
Nucleotides with >20x sequencing coverage (%) 99.4%

Bioinformatics

The target region for each gene includes coding exons and ±20 base pairs from the exon-intron boundary. In addition, the panel includes non-coding variants if listed above (Non-coding variants covered by the panel). Some regions of the gene(s) may be removed from the panel if specifically mentioned in the ‘Test limitations” section above. The sequencing data generated in our laboratory is analyzed with our proprietary data analysis and annotation pipeline, integrating state-of-the art algorithms and industry-standard software solutions. Incorporation of rigorous quality control steps throughout the workflow of the pipeline ensures the consistency, validity and accuracy of results. Our pipeline is streamlined to maximize sensitivity without sacrificing specificity. We have incorporated a number of reference population databases and mutation databases such as, but not limited, to 1000 Genomes Project, gnomAD, ClinVar and HGMD into our clinical interpretation software to make the process effective and efficient. For missense variants, in silico variant prediction tools such as SIFT, PolyPhen, MutationTaster are used to assist with variant classification. Through our online ordering and statement reporting system, Nucleus, the customer has an access to details of the analysis, including patient specific sequencing metrics, a gene level coverage plot and a list of regions with inadequate coverage if present. This reflects our mission to build fully transparent diagnostics where customers have easy access to crucial details of the analysis process.

Clinical interpretation

We provide customers with the most comprehensive clinical report available on the market. Clinical interpretation requires a fundamental understanding of clinical genetics and genetic principles. At Blueprint Genetics, our PhD molecular geneticists, medical geneticists and clinical consultants prepare the clinical statement together by evaluating the identified variants in the context of the phenotypic information provided in the requisition form. Our goal is to provide clinically meaningful statements that are understandable for all medical professionals regardless of whether they have formal training in genetics.

Variant classification is the corner stone of clinical interpretation and resulting patient management decisions. Our classifications follow the Blueprint Genetics Variant Classification Schemes based on the ACMG guideline 2015. Minor modifications were made to increase reproducibility of the variant classification and improve the clinical validity of the report. Our experience with tens of thousands of clinical cases analyzed at our laboratory allowed us to further develop the industry standard.

The final step in the analysis of sequence variants is confirmation of variants classified as pathogenic or likely pathogenic using bi-directional Sanger sequencing. Variant(s) fulfilling all of the following criteria are not Sanger confirmed: 1) the variant quality score is above the internal threshold for a true positive call, 2) an unambiguous IGV in-line with the variant call and 3) previous Sanger confirmation of the same variant at least three times at Blueprint Genetics. Reported variants of uncertain significance are confirmed with bi-directional Sanger sequencing only if the quality score is below our internally defined quality score for true positive call. Reported copy number variations with a size <10 exons are confirmed by orthogonal methods such as qPCR if the specific CNV has been seen less than three times at Blueprint Genetics.

Our clinical statement includes tables for sequencing and copy number variants that include basic variant information (genomic coordinates, HGVS nomenclature, zygosity, allele frequencies, in silico predictions, OMIM phenotypes and classification of the variant). In addition, the statement includes detailed descriptions of the variant, gene and phenotype(s) including the role of the specific gene in human disease, the mutation profile, information about the gene’s variation in population cohorts and detailed information about related phenotypes. We also provide links to the references used, congress abstracts and mutation databases to help our customers further evaluate the reported findings if desired. The conclusion summarizes all of the existing information and provides our rationale for the classification of the variant.

Identification of pathogenic or likely pathogenic variants in dominant disorders or their combinations in different alleles in recessive disorders are considered molecular confirmation of the clinical diagnosis. In these cases, family member testing can be used for risk stratification within the family. In the case of variants of uncertain significance (VUS), we do not recommend family member risk stratification based on the VUS result. Furthermore, in the case of VUS, we do not recommend the use of genetic information in patient management or genetic counseling.

Our interpretation team analyzes millions of variants from thousands of individuals with rare diseases. Thus, our database, and our understanding of variants and related phenotypes, is growing by leaps and bounds. Our laboratory is therefore well positioned to re-classify previously reported variants as new information becomes available. If a variant previously reported by Blueprint Genetics is re-classified, our laboratory will issue a follow-up statement to the original ordering health care provider at no additional cost.