CMA – Kromozomal Mikroarray

Kromozomal seviyede delesyon ve duplikasyonların değerlendirildiği CNV analizi için, CMA altın standarttır

Genel Bakış

Raporlama

Metodoloji

Örnek Talepleri

Sınırlamalar

CMA Genel Bakış

CMA
Talep
Endikasyonlar

CGH olarak da bilinen kromozomal mikroarray analizi (CMA), genom boyunca klinik olarak önemli majör kromozom dengesizliklerini (anöploidiler) ve submikroskobik (mikrodelesyon/mikroduplikasyon) kopya sayısı varyasyonlarını tespit edebilen bir tanı testidir.
Kromozomal mikroarray analizi tüm genomda delesyon ve duplikasyonların saptanması için altın standarttır.
CMA, karyotiplemenin tespit edemediği küçük bölgeleri görselleştirmeye izin veren submikroskobik çözünürlük sağlar. CMA’nın duyarlılığı, kullanılan moleküler probların sayısına ve bunların genom kapsamına bağlıdır. Prob sayısı ne kadar fazla olursa (180K, 400K, 750K…), hassasiyet de o kadar yüksek olur.

CMA can detect:

Small chromosomal microdeletions and duplications
Copy number variations
Numerical chromosomal aneuploidy
Unbalanced rearrangements
Excessive homozygosity – platform dependent
Suggestive risk of inheriting recessive disease or imprinting disorders – platform dependent
Triploidy and tetraploidy – platform dependent
Mosaicism greater than 20-30%

Preconception

CMA can be offered in the pre-conception phase if one or more of the below indications are present:

If a previous affected child presents with a normal karyotype or WES, but a genetic condition is suspected..
To check whether a copy number variation that was detected in the affected child is de novo or inherited from their parents.

Constitutional karyotyping in both parents is always recommended when a balanced chromosomal rearrangement is suspected (i.e. Recurrent miscarriages, infertility,..)

Prenatal

CMA is offered prenatally if one or more of the below indications are present:

Abnormal fetal ultrasound
Abnormal NIPT results indicated an increased risk of a chromosomally abnormal fetus
Abnormal high-risk maternal serum screen
The parents have a known chromosomal rearrangement, mosaicism or previous aneuploidies
The parents have had previous livebirths or stillbirths with chromosomal abnormalities
Fetal congenital abnormalities detected with ultrasound or MRI that indicate a significant risk of an unbalanced chromosomal abnormality
Apparently balanced inherited rearrangements in a fetus with congenital abnormalities.
Apparently balanced de novo rearrangements identified by G-band analysis (karyotype)
High risk pregnancies

Post-natal

CMA is offered in childhood or adulthood if one or more of the below indications are present – the chromosomal microarray can be considered as a first line test in the following

If an individual or fetus presents with multiple congenital anomalies that are not specific to a well identified genetic syndrome
If a karyotype is negative and the individual’s phenotype is indicative of chromosomal aneuploidy.
If an individual or fetus present with apparently nonsyndromic developmental delay or intellectual disabilities
If an individual presents with autism spectrum disorders
If a fetus is malformed or a still birth of unknown aetiology occurs

The CMA can be used in cases where other tests have failed to yield a diagnosis specifically if one or more of the below symptoms or conditions are present

Unexplained seizure disorder
Growth delay
Psychiatric illness
Neuromuscular conditions
Neuromuscular conditions
Skeletal dysplasia
Short stature
Excessive growth
Microcephaly
Macrocephaly

Product of Conception

CMA can be offered on a product of conception sample if there was a case of spontaneous abortion.

CMA Raporlama & Sonuçlar

Igenomix’te farklı CMA türleri mevcuttur:

CMA HD (en hassas test)

Kopya numarası probu (1.9 milyon) + SNP (750 K).
Tüm genom kapsamı
Düşük heterozigotluk, uniparental dizomi (UPD), düşük seviye mozaisizm ve numune heterojenliği bölgeleri tespit edilir
En yüksek prob yoğunluğu

CMA 750K (en uygun maliyetli test)

Copy number probes only (550K) + SNP (200 K)
Emphasis on clinically relevant regions
Identification of regions of excessive homozygosity indicating UPD, may suggest consanguinity and determine candidate genes for further testing

CMA Örnek Talepleri

Tüpün üzerindeki bilgilerin eksiksiz bir şekilde doldurulup, etiketlenmesi gerekir. Yanlış etiketleme numunenin reddedilmesine neden olabilir. Numunenin kabul edilmesi için hastanın tam adı, doğum tarihi, cinsiyeti ve tıbbi kayıt numarası gereklidir.

Anne kan örneği, CVS ve amniyon örnekleri ile birlikte gönderilmelidir.
Doğum öncesi numunelere öncelik verilecektir.

“Bilgilendirilmiş Onam Formu” ve Test Talep Formu” (gönderilen kitin içinde bulunur) hasta tarafından uygun şekilde doldurulmalı, imzalanmalı ve numunelerle birlikte gönderi kutusunun içerisinde veya e-mail ile laboratuvara gönderilmelidir. Kit ve gönderi için gerekli taşıma evrakları Igenomix tarafından hazırlanır ve hastaya gönderilir.

CMA Metodoloji

Deletions smaller than 50 kb and duplications smaller than 400 kb may not be detected. Detected copy number variations (CNVs) are reported when found to have clear or suspected clinical relevance; CNVs devoid of relevant gene content or reported as common findings in the general population may not be reported. Regions of homozygosity are reported when a single LCSH is greater than 8-15 Mb (dependent upon chromosomal location and likelihood of imprinting disorder), or when the total autosomal LCSH proportion is greater than 3% (only autosomal LCSH greater than 3 Mb are considered for this estimate). Genomic linear positions are given relative to NCBI build 37 (hg19).

Test results are interpreted based on the recommendations and guidelines of International Standard of Cytogenomics Arrays (ISCA) as described below:

Positive (Pathogenic and likely pathogenic)

A positive result indicates that a copy number variant has been identified in association with the disease phenotype under study. This scenario will allow to provide genetic counselling or personal guidance regarding possible medical treatments, disease progression, reproductive-/prevention-strategies and potential implications for other family members.

Negative:

A negative result indicates that no disease-causing copy number variation was identified in the test performed. This does not guarantee that the induvial will be healthy or free from other genetic disorders or medical conditions. Additionally, a negative result does not rule out a genetic cause of the disease nor does it eliminate the risk for future offspring. However, if a negative test result is obtained and the variant in question is known to be present in affected family members, this then rules out a diagnosis of that genetic disorder in the proband. A negative result may be explained by several causes, including limited genetic knowledge and limitations associated to the used methodology.

Inconclusive / Variant of Uncertain Significance (VUS):

A finding of a variant of uncertain significance indicates that a copy number variation was detected, but it is currently unknown whether that CNV is associated with a genetic disorder or disease. A variant of uncertain significance is not the same as a positive result and does not clarify whether the proband is at an increased risk to develop a genetic disorder or disease.
The change could be a normal genetic variant, or it could be disease-causing. Further analysis may be recommended, including testing both parents as well as other affected and unaffected family members. Sometimes, performing ancillary tests is necessary to prove the phenotype that the proband presents with. Detailed medical records or information from other family members also may be needed to help clarify the result.
Result interpretation is based on currently available information in the medical literature, research, and scientific databases. Because the literature, medical and scientific knowledge are constantly changing, new information that becomes available in the future may replace or add to the information that Igenomix used to interpret the results. Re-analysis of the results in previously issued reports considering new evidence is not routinely performed but is available upon request.

CMA Sınırlamalar

CMA cannot identify:
- Balanced chromosomal rearrangements (balanced translocations, inversions)
- Small changes in the sequence of single genes (point mutations)
- Tiny duplications and deletions of DNA segments within a single gene (Fragile X syndrome, for example)
- Uniparental disomy (UPD)
- Methylation alterations
- Mosaicism less than 20%
- Complete ploidy

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