Faravareh Khordadpoor (PhD in molecular genetics) 1- Tehran Medical Genetics Laboratory 2- Science and research branch, Islamic Azad University

Transcription

1 Faravareh Khordadpoor (PhD in molecular genetics) 1- Tehran Medical Genetics Laboratory 2- Science and research branch, Islamic Azad University مشاوره ژنتیک و نقش آن در پیش گیری از معلولیت ها 20 مرداد و 1

2 CMA is a technology used to determine if there are small extra (micro-duplication) or missing (micro-deletion) pieces of genetic information. These gains and losses are called copy number variants (CNVs). Developmental delay Intellectual disabilities Congenital anomalies (heart defects, primary microcephaly, short stature and failure to thrive, etc.) Autistic spectrum disorders Cancer studies 2

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7 CMA Methodology Analyze Cy3/Cy5 fl of patient t Cy3/Cy5 ratio >1 Duplication Cy3/Cy5 ratio <1 Deletion 7

8 Log 2 -ratio Xp21 Complex Glycerol Kinase Deficiency 6.66 Mb deletion Start: End: X chromosome 8

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13 CNVs are common in all genomes surveyed Blue = pathogenic Red = deletion Green = duplication 13

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18 He had MR, speech delay, dermatitis, macrocephaly, round face, low hair line, broad cheeks, prominent maxilla, hypertlorism, upslanting palpebral fissures, retrognathia, epicanthic folds, glaucoma/ buphthalmos, broad nasal bridge, abnormal nasal septum, small and downturned mouth, thick lips, high vaulted and narrow palate, tooth crown shape abnormality, oligodontia, dental caries, flat philtrum, posterior angulation of ears, anteverted/ bat ears, ear lobe abnormal size, short neck, umbilical hernia, inguinal hernia, scoliosis, lordosis, large hand, small penis, coxavara, coloboma of the eyelid, abnormally placed nipples, umbilical hernia, mild arachnodactyly, large foot, overlapping toes and knock knees- genu valgum 18

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22 The three basic designs in acgh DNA probes in a whole genome or constitutive array represent sequences that are approximately evenly spaced across the length of a chromosome. Targeted arrays have probes corresponding to genes of interest and disproportionately represent exons or coding sequences. The lower panel shows a combination design that is a constitutive array with limited targeted genes. The widely spaced probes along the chromosomes are termed backbone probes 22

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28 Indication Advanced maternal age, multiple soft markers on ultrasound, ultrasound anomaly, positive prenatal screen, etc. Genetic counselling with testing options No further testing Karyotype Invasive Testing (diagnostic) QF-PCR Detects common aneuploidies: Down syndrome, Trisomy 18, Trisomy 13 and sex chromosome aneuploidies Screening Test e.g. NIPT If positive If negative Depending on indication: No further testing Consider additional testing Additional Testing e.g. Chromosomal microarray 28

29 A systematic review of the literature was conducted to calculate the utility of prenatal microarrays in the presence of a normal conventional karyotype. 12,362 cases from all prenatal ascertainment groups 1 i.e. abnormal ultrasound, advanced maternal age, prenatal screening, parental anxiety 2.4% had a clinically significant copy number variant (CNV) (295/12,362) 3,090 abnormal ultrasound 1 6.5% had clinically significant CNV (201/3,090) Variant of Unknown significance (VUS) are found in about 1% of cases 2,3 4,164 other indications 1 1.1% had clinically significant CNV (44/4,164) [1] Callaway et al 2013 Prenat Diagn [2] Shaffer et al 2012 Prenat Diagn [3] Wapner et al 2012 NEJM 5,108 AMA 1 1.0% had clinically significant CNV (50/51,08) 29

30 Normal No copy number variant (microdeletion/microduplication) detected Does not exclude a syndrome caused by a mutation within a single gene or detect a balanced translocation Pathogenic Copy Number Variant has been previously described and associated with a known phenotype Incidental finding Results that are not apparently relevant to indication for which test was ordered Variant of uncertain significance (VOUS/VUS) Not yet described in the literature, is challenging to interpret and benefits from knowledge of parental status 30

31 VUS identified in fetus Test parents Neither parent has the VUS identified in the pregnancy (both have a normal result) Barring nonpaternity, the finding in fetus is new, de novo, and likely pathogenic One parent has same CMA result as child Finding in the fetus is pathogenic, and the parent displays reduced penetrance (not everyone with the CNV will have symptoms), variable expressivity (individuals with this CNV have varied presentation) Finding in the fetus is a normal familial variant and not pathogenic 31

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33 There is variability in practice with regards to who will be offered CMA Consent process, pre- and post- test counselling are complicated A description of the test The type of sample required Potential benefits and limitations of testing The possible outcomes of testing. An informed consent document Need the parental samples Positive results Negative results 33

34 Take a family history to identify familial and/or ethnicity-specific disorders and screen accordingly Consider consanguinity and screen and test accordingly Refer or consult genetics when in doubt 34

35 September 28, 2010 ACMG Recommends Replacing Karyotyping with Chromosomal Microarrays as 'First-Line' Postnatal Test Microarrays should be used instead of G- banded karyotyping as the first test to detect genetic abnormalities in postnatal evaluations, according to the American College of Medical Genetics. 35

36 Microduplication of an Entire Single PTCH1 gene Gene 360 kb duplication in 9q22.32 In a 21-month-old boy with developmental delay, failure to thrive, and microcephaly. The same duplication was identified in his mother who had microcephaly and mild intellectual delays. 36

37 Duplication Involving the 5ʹ A gain of 33 oligos covering the 5ʹ portion of the b isoform of the NRXN1 gene on chromosome 2p16.3 End of the Gene In a patient with pervasive developmental delay and autism. This duplication was not found in the patient s mother; the patient s biological father was not available for analysis. 37

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44 44 با تشکر از توجه شما