{"id":356,"date":"2025-06-13T09:41:00","date_gmt":"2025-06-13T08:41:00","guid":{"rendered":"https:\/\/services.nhslothian.scot\/geneticservice\/cytogenomic-tests\/"},"modified":"2025-06-13T09:43:15","modified_gmt":"2025-06-13T08:43:15","slug":"cytogenomic-tests","status":"publish","type":"page","link":"https:\/\/services.nhslothian.scot\/geneticservice\/cytogenomic-tests\/","title":{"rendered":"Cytogenomic Tests"},"content":{"rendered":"\n<p><\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><em>Microarray<\/em>s<\/h2>\n\n\n\n<p>Tel: 0131 537 1183<\/p>\n\n\n\n<p><\/p>\n\n\n\n<p><strong><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">POSTNATAL<\/mark><\/strong><\/p>\n\n\n\n<p>Microarray testing requests are welcome from Clinical Genetics, Paediatrics or Psychiatrists for Adults with Learning Disability, only for patients with;<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Congenital malformation\/abnormalities<\/li>\n\n\n\n<li>Dysmorphic features<\/li>\n\n\n\n<li>Failure to thrive in babies<\/li>\n\n\n\n<li><em>Confirmed diagnosis<\/em> of moderate to severe intellectual disability or of moderate to severe autism spectrum disorder<\/li>\n\n\n\n<li>Epilepsy<\/li>\n<\/ul>\n\n\n\n<p>or with <strong>significant<\/strong> delay in one or more of the following developmental areas;<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Gross motor<\/li>\n\n\n\n<li>Vision and fine motor<\/li>\n\n\n\n<li>Hearing, speech and language<\/li>\n\n\n\n<li>Social, emotional and behavioural<\/li>\n<\/ul>\n\n\n\n<p>For referrals with limited clinical details, blood samples in both lithium heparin and EDTA will be processed and stored and an attempt will be made to contact the referring clinician for more details.   If microarray testing is then considered appropriate, testing will be actioned.   Repeat samples will not be necessary.<\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">PRENATAL<\/mark><\/h5>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Solid Tissue samples where there is a fetal anomaly\/parental chromosomal rearrangement\/history of recurrent miscarriage (sample should be processed by Pathology first).<\/li>\n\n\n\n<li>Characterisation of prenatal abnormalities (e.g abnormal ultrasound or increased risk from Serum Screen)<\/li>\n<\/ul>\n\n\n\n<h5 class=\"wp-block-heading\"><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">ACQUIRED<\/mark><\/h5>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Characterisation of Tumour samples e.g 1p19q co-deletions, MYC amplifications, TP53 deletions etc<\/li>\n<\/ul>\n\n\n\n<p><\/p>\n\n\n\n<h4 class=\"wp-block-heading\">Specimen Requirements<\/h4>\n\n\n\n<p>Two specimen tubes are required; one a lithium Heparin specimen tube, the other an EDTA (KE) tube.  Arrange for immediate transport to the Cytogenetics Laboratory. if this is not available, blood specimens should be refrigerated. (DO NOT FREEZE)  Referring clinicians are requested to comply with NHS Lothian policy on <a href=\"https:\/\/services.nhslothian.scot\/geneticservice\/mandatory-datasets\/\" data-type=\"page\" data-id=\"353\">Mandatory Data Sets<\/a>:  Failure to do so will result in delays in processing or rejection of the sample.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-356_e597c4-a1 .kt-block-spacer{height:30px;}.wp-block-kadence-spacer.kt-block-spacer-356_e597c4-a1 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-356_e597c4-a1\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\" \/><\/div><\/div>\n\n\n\n<div class=\"wp-block-getwid-icon\"><div class=\"wp-block-getwid-icon__wrapper\"><i class=\"far fa-sun\"><\/i><\/div><\/div>\n\n\n\n<p><strong><mark>TARGETED XON LEVEL ARRAYS<\/mark><\/strong><\/p>\n\n\n\n<p>High resolution XON array analysis is available for the following clinical situations (only where an appropriate MLPA test is not available);<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Confirmatory testing of a CNV identified using another method such as CNVs detected through NGS, or analysis with a different array type\/platform, where confirmation\/refinement of gene involvement is required.   <\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Identification of a \u2018second hit\u2019 where a single pathogenic sequence variant has been identified in an autosomal recessive gene, and the phenotype of the patient is a good fit for this gene. <\/li>\n<\/ul>\n\n\n\n<ul class=\"wp-block-list\">\n<li>The clinician has a strong clinical suspicion of a particular disorder which can be caused by variants in one or a small number of genes, ideally for which CNVs have been reported in the literature.<\/li>\n<\/ul>\n\n\n\n<p>These cases should be discussed and agreed at the Scottish dysmorphology meeting before a request to the lab is made.<\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-356_f5d233-42 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-356_f5d233-42 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-356_f5d233-42\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\" \/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><em>FISH (Fluorescent In Situ Hybridisation)<\/em><\/h2>\n\n\n\n<p>Tel: 0131 537 2985<\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">STRUCTURAL ABNORMALITIES<\/mark><\/h5>\n\n\n\n<p>Complex chromosome rearrangements and sub-microscopic rearrangements can be studied by molecular cytogenetic techniques using chromosome paints.<\/p>\n\n\n\n<h5 class=\"wp-block-heading\"><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">CANCER CYTOGENETICS<\/mark><\/h5>\n\n\n\n<p>The same techniques used to study structural abnormalities and aneuploidy in constitutional samples can also be used to study cancer cells. There are specific probes available to detect gene fusions that have arisen as a result of the rearrangement of specific genetic material.<\/p>\n\n\n\n<p>Gene fusions currently detectable by FISH include:<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>BCR\/ABL in chronic myeloid leukaemia<\/li>\n\n\n\n<li>PML\/RARA in acute promyelocytic leukaemia<\/li>\n\n\n\n<li>ETV6\/RUNX1 in acute lymphoblastic leukaemia<\/li>\n\n\n\n<li>t(14;18) in follicular lymphoma<\/li>\n<\/ul>\n\n\n\n<p>View the <a href=\"https:\/\/services.nhslothian.scot\/geneticservice\/repertoire-of-tests\/\" data-type=\"page\">Repertoire of tests<\/a><\/p>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-356_c76e29-d7 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-356_c76e29-d7 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-356_c76e29-d7\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\" \/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><em>QF-PCR<br>(Quantitative Fluorescence Polymerase Chain Reaction)<\/em><\/h2>\n\n\n\n<p>Small sections of DNA from the sample are amplified, labelled with fluorescent tags and the amounts measured by electrophoresis.<\/p>\n\n\n\n<p>QF-PCR is used to measure gene dosage. It can be used to test for aneuploidy of whole chromosomes.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>For <mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\"><strong>PRENATAL\/TISSUE<\/strong><\/mark> samples aneuploidy for chromosomes 13,18,21,X and Y are tested<\/li>\n\n\n\n<li>For<strong> <mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">NEONATAL BLOOD<\/mark><\/strong>: The laboratory offers a rapid aneuploidy test for Chromosome 21.    <\/li>\n<\/ul>\n\n\n<style>.wp-block-kadence-spacer.kt-block-spacer-356_d4b1a5-45 .kt-block-spacer{height:60px;}.wp-block-kadence-spacer.kt-block-spacer-356_d4b1a5-45 .kt-divider{border-top-width:1px;height:1px;border-top-color:#eee;width:80%;border-top-style:solid;}<\/style>\n<div class=\"wp-block-kadence-spacer aligncenter kt-block-spacer-356_d4b1a5-45\"><div class=\"kt-block-spacer kt-block-spacer-halign-center\"><hr class=\"kt-divider\" \/><\/div><\/div>\n\n\n\n<h2 class=\"wp-block-heading\"><em>Male Factor Infertility Kit<\/em><\/h2>\n\n\n\n<p>Y chromosomal microdeletions are the second most common cause of male infertility after Klinefelter\u2019s syndrome with deletion frequencies varying between 2 and 10% in azoospermic men, dependent on patient selection (Krausz et al., 2023). Clinically relevant deletions have been identified in three regions of the Y chromosome, AZFa, AZFb and AZFc.<\/p>\n\n\n\n<ul class=\"wp-block-list\">\n<li>Testing of <strong><mark style=\"background-color:#EFFFBF\" class=\"has-inline-color has-standard-black-color\">Y MICRODELETION<\/mark><\/strong> by QF-PCR is available for patients with  azoospermia (sperm concentrations &lt; 2&#215;10^6\/ml).<\/li>\n<\/ul>\n\n\n\n<p>Please note: This test requires 2-5mL of peripheral blood in an EDTA tube.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Microarrays Tel: 0131 537 1183 POSTNATAL Microarray testing requests are welcome from Clinical Genetics, Paediatrics or Psychiatrists for Adults with Learning Disability, only for patients with; or with significant delay in one or more of the following developmental areas; For referrals with limited clinical details, blood samples in both lithium heparin and EDTA will be<\/p>\n","protected":false},"author":2,"featured_media":0,"parent":0,"menu_order":36,"comment_status":"closed","ping_status":"closed","template":"page-templates\/widewidth.php","meta":{"footnotes":""},"categories":[],"class_list":["post-356","page","type-page","status-publish","hentry"],"rttpg_featured_image_url":null,"rttpg_author":{"display_name":"NHS Lothian","author_link":"https:\/\/services.nhslothian.scot\/geneticservice\/author\/nhs-lothian\/"},"rttpg_comment":0,"rttpg_category":false,"rttpg_excerpt":"Microarrays Tel: 0131 537 1183 POSTNATAL Microarray testing requests are welcome from Clinical Genetics, Paediatrics or Psychiatrists for Adults with Learning Disability, only for patients with; or with significant delay in one or more of the following developmental areas; For referrals with limited clinical details, blood samples in both lithium heparin and EDTA will be","_links":{"self":[{"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/pages\/356","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/comments?post=356"}],"version-history":[{"count":14,"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/pages\/356\/revisions"}],"predecessor-version":[{"id":1382,"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/pages\/356\/revisions\/1382"}],"wp:attachment":[{"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/media?parent=356"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/services.nhslothian.scot\/geneticservice\/wp-json\/wp\/v2\/categories?post=356"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}