Introduction

Cytogenetic investigations are performed on a wide range of referrals for the investigation of structural and numerical chromosome abnormalities and utilise a variety of laboratory techniques. Samples follow a particular testing pathway according to the referral reason and, in some cases, in response to the results of preliminary tests.

Chromosome analysis and Fluorescence In Situ Hybridisation (FISH) are used as front line tests to detect balanced structural chromosome rearrangements such as translocations and inversions, to investigate sex chromosome abnormalities or mosaicism. They may also be used for some family studies or as secondary tests to aid interpretation of other investigations.

Referral information

We accept blood samples for cytogenetic investigations from babies with ambiguous genitalia, suspected aneuploidies (trisomy 21, trisomy 13 or trisomy 18), for confirmation of a chromosome abnormality detected prenatally or for suspected sex chromosome aneuploidy. We also accept referrals from couples who are undergoing tests for infertility (IVF couples, azoospermic males) and patients with problems of sexual development, delayed/premature puberty or premature ovarian failure. We accept referrals for follow-up studies after the detection of a chromosome abnormality either in another family member or following a pregnancy loss. We also accept referrals for patients with a family history of a balanced rearrangement (inversion, insertion or translocation). Samples from babies under the age of three months and from expectant couples are classed as urgent samples (see reporting times).

We accept skin punch biopsy samples from patients referred with suspected mosaicism (e.g. Hypomelanosis of Ito or suspected Pallister-Killian syndrome). Skin biopsies should be taken from two areas for mosaicism studies.

View full test details for Cytogenetic Investigations

Introduction

Down syndrome (trisomy 21) occurs in approximately 1 in 1000 live births, making it the most common aneuploidy. It occurs in individuals who carry an extra chromosome 21 or extra chromosome 21 material, including the critical region at 21q22.3. The main features characteristic of trisomy 21 include distinctive facial features, mild to severe learning difficulties, congenital heart defects (particularly AVSD), gastrointestinal problems (such as duodenal atresia or stenosis), imperforate anus and Hirschsprung Disease. Facial features include down-slanting palperbral fissures, a flattened profile, Brushfield spots and a protruding tongue. The majority of cases are “free” trisomy 21, but in approximately 3-5% of cases the additional chromosome 21 material is the result of a derivative chromosome 21, which may be inherited from one parent who carries a balanced reciprocal translocation involving chromosome 21. Although free trisomy 21 occurs sporadically, there is an increased risk of a Down syndrome pregnancy with increasing maternal age. Trisomy 21 may also appear in a mosaic form, where normal cells are also present in the individual. These individuals may exhibit a milder phenotype, which is dependent on the extent and tissue distribution of the normal cell line.

Referral information

For prenatal referrals we accept samples from women that have a high risk (>1:150) following antenatal screening including Combined or Quadruple testing, a family history of a chromosome rearrangement predisposing to trisomy 21, a previously affected pregnancy, or ultrasound scan findings indicative of trisomy 21. For postnatal samples, we accept referrals from patients with appropriate clinical features for a diagnosis of trisomy 21 or for the confirmation of a prenatal diagnosis.

View full test details for Down Syndrome

Introduction

Edwards Syndrome (trisomy 18), occurs in approximately 1 in 5000 live births. It is caused by an additional chromosome 18 or extra chromosome 18 material, including the critical region at 18q11-q12. The main features of Edwards syndrome include low birth weight, abnormally shaped head (microcephaly), hypotonia, characteristic facial features (such as small jaw, upturned nose, widely spaced eyes and malformed ears), rockerbottom feet, overlapping fingers and other congenital abnormalities of the heart, brain, kidneys, digestive tract and genitals. Many infants with trisomy 18 die within the first month and only 10% survive to one year. Although free trisomy 18 occurs sporadically, there is an increased risk of an Edwards syndrome pregnancy with increasing maternal age. Trisomy 18 may also appear in a mosaic form, where normal cells are also present in the individual. These individuals may exhibit a milder phenotype, which is dependent on the extent and tissue distribution of the normal cell line.

Referral information

For prenatal referrals we accept samples from women that have a high risk (>1:150) following antenatal screening including Combined or Quadruple testing, a family history of a chromosome rearrangement predisposing to trisomy 18, a previously affected pregnancy, or ultrasound scan findings indicative of trisomy 18. For postnatal samples we accept referrals from patients with appropriate clinical features for a diagnosis of trisomy 18 or for the confirmation of a prenatal diagnosis.

View full test details for Edwards Syndrome

Introduction

Klinefelter syndrome has a prevalence of approximately 1 in 500 males. It results from the gain of an additional X chromosome in each cell, giving a 47,XXY male karyotype. The features are mild, children may present with small testes, small penis, hypospadias or cryptorchidism (undescended testes). They may have learning disabilities and difficulty with speech and language development. At puberty boys with Klinefleter syndrome can develop breast enlargement (gynecomastia), have reduced facial and body hair, tall stature and hypogonadism. Individuals with Klinefelter syndrome are invariably infertile and may present with azoospermia. Klinefelter syndrome cases arise as a sporadic event. However, 46,XX males have also been described with features of Klinefelter syndrome. In this case the syndrome results from the translocation of Y material (including the sex determining region, SRY) to the X chromosome during paternal meiosis. Klinefelter syndrome can also appear in a mosaic form, where normal cells are also present in the individual (a 47,XXY/46,XY karyotype). These individuals may exhibit a milder phenotype, which is dependent on the extent and tissue distribution of the normal cell line.

Referral information

We accept postnatal blood samples from males with appropriate clinical features for a diagnosis of Klinefelter syndrome. Klinefelter syndrome may also be discovered as an incidental finding in prenatal cases or samples following pregnancy loss.

View full test details for Klinefelter Syndrome

Introduction

Identifying the sex of a fetus is important in the clinical management of pregnancies where there is a risk of an X-linked genetic disorder or intrauterine treatment is dependent on the sex of the fetus. Fetal sex can be determined by isolating cell free fetal DNA (ffDNA) from maternal blood plasma and testing for the presence or absence of Y chromosome sequences.

Referral information

16ml of blood may be taken into EDTA from pregnant women of at least 9 weeks gestation. Please notify the laboratory at least one week before the sample is to be taken (contact the Duty Scientist on 0161 276 6553 with the patient name, reason for referral, gestation and when the sample will arrive at the laboratory). Testing may be delayed if notice is not provided.  Samples should arrive at the laboratory within 24 hours of collection.

View full test details for Non-Invasive Fetal Sex Determination

Introduction

Patau Syndrome (trisomy 13) occurs in approximately 1 in 16000 live births. It is caused by an additional chromosome 13 or extra chromosome 13 material. The features commonly associated with trisomy 13 include a number of midline defects such as cleft lip and palate, holoprosencephaly, microphthalmia and hypertelorism, (small, wide-spaced eyes) and microcephaly (small head). Also common are extra fingers and/or toes, hypotonia, heart, brain, and spinal cord abnormalities. Approximately 80% of infants born with trisomy 13 do not survive the first month of life. The majority of cases are “free” trisomy 13, but in approximately 20% of cases the additional chromosome 13 material is derived from a translocation, which may or may not be inherited from a parent. Although free trisomy 13 occurs sporadically, there is an increased risk of a Patau syndrome pregnancy with increasing maternal age. Trisomy 13 may also appear in a mosaic form, where normal cells are also present in the individual. These individuals may exhibit a milder phenotype, which is dependent on the extent and tissue distribution of the normal cell line.

Referral information

For prenatal referrals we accept samples from women that have a high risk (>1:150) following antenatal screening including Combined or Quadruple testing, a family history of a chromosome rearrangement predisposing to trisomy 13, a previously affected pregnancy, or ultrasound scan findings indicative of trisomy 13. For postnatal samples we accept referrals from patients with appropriate clinical features for a diagnosis of trisomy 13 or for the confirmation of a prenatal diagnosis.

View full test details for Patau Syndrome

Introduction

The NHS fetal anomaly screening programme (FASP) provides screening for fetal anomalies to all pregnant women in the UK. This includes an ultrasound scan as part of the Combined test between 10 and 14 weeks gestation, measuring fetal nuchal translucency, and a fetal anomaly scan between 18 and 20 weeks gestation. Where nuchal translucency measurements are above 3.5mm in the first trimester or 6mm in the second trimester or other fetal structural or growth abnormalities are identified by scan, women are offered an invasive prenatal diagnostic test. This laboratory will carry out an initial rapid Quantitative Fluorescent PCR (QF-PCR) test on the sample to exclude trisomy 13, 18 and 21 (Patau, Edwards and Down syndromes respectively), triploidy, and Turner syndrome where there is a raised nuchal translucency or other clinical indication. G-banded chromosome analysis is performed where aneuploidy is identified to confirm the finding and give an indication of the risk of recurrence in future pregnancies. Samples that show a normal result by QF-PCR will be tested by microarray analysis to look for genomic imbalances that may explain the cause of fetal abnormalities. Testing may be performed on either chorionic villi (between 11 and 14 weeks gestation) or amniotic fluid (after 15 weeks gestation). QF-PCR results will usually be available via the antenatal clinic within three days and microarray or chromosome analysis results within fourteen calendar days.

Referral information

We accept prenatal referrals (chorionic villus and amniotic fluid samples) from pregnant women where ultrasound scanning has identified a nuchal translucency measurement of greater than 3mm in the first trimester or 6mm in the second trimester, there is intrauterine growth restriction without placental insufficiency or the scan has identified one or more fetal structural abnormalities. Samples from women with a known family history of a chromosome rearrangement will be tested by microarray or G-banded chromosome analysis, depending on the rearrangement.

View full test details for Prenatal - Abnormal Ultrasound Scan Findings

Introduction

The NHS fetal anomaly screening programme (FASP) provides screening for fetal anomalies as well as Down, Edwards and Patau syndromes to all pregnant women in the UK. Women are offered the Combined test between 10 and 14 weeks gestation which measures fetal nuchal translucency by ultrasound scan and pregnancy associated proteins in maternal blood serum. Patients presenting later in pregnancy are offered the Quadruple test measuring maternal serum only. The screening test gives a risk of the pregnancy being affected with Down, Edwards or Patau syndromes. Where this risk is high (greater than 1 in 150), an invasive prenatal diagnostic test is offered. This involves either chorionic villus sampling (between 11 and 14 weeks gestation) or an amniocentesis (after 15 weeks gestation). This laboratory will carry out a rapid Quantitative Fluorescent PCR (QF-PCR) test on the sample to diagnose or exclude trisomy 13, 18 and 21 (Patau, Edwards and Down syndrome respectively). Results will usually be available via the antenatal clinic within three working days. Chromosome analysis is performed where trisomy is identified to confirm the finding and give an indication of the risk of recurrence in future pregnancies.

Referral information

We accept prenatal referrals (chorionic villus and amniotic fluid samples) from pregnant women with a high risk of trisomy 13, 18 or 21 (Patau, Edwards and Down syndromes respectively), either following antenatal screening, a previous aneuploid pregnancy or due to a known familial chromosome rearrangement predisposing to trisomy 13, 18 or 21.

View full test details for Prenatal - Increased Risk of Down, Edward or Patau Syndrome Following Screening

Introduction

Quantitative-Fluorescent PCR (QF-PCR) is a rapid molecular test for the identification of common aneuploidy syndromes, specifically chromosomes 13, 18 and 21 and the sex chromosomes.

Referral information

QF-PCR testing is carried out for aneuploidies 13, 18 and 21 on all chorionic villus and amniotic fluid samples unless the sample is too small, unsuitable, or the test is specifically not requested. Sex chromosome aneuploidy is carried out on chorionic villus and amniotic fluid samples if cystic hygroma or raised nuchal translucency is detected on ultrasound scan.  Samples that do not meet the criteria for microarray analysis are tested by QF-PCR only. Samples that meet the requirements for microarray analysis should be accompanied by a maternal blood sample in EDTA to exclude maternal cell contamination.

QF-PCR is performed on fetal tissue samples for confirmation of a prenatal result and as the first tier test for pregnancy loss samples that fall within our Acceptance Criteria.

QF-PCR testing is also performed on blood samples from new-born babies where an aneuploidy is suspected (trisomy 13, 18 or 21) or for those with ambiguous genitalia (sex chromosome testing).

View full test details for Rapid QF-PCR Testing

Introduction

In about 2-5% of couples with a history of recurrent miscarriage, one partner carries a balanced chromosome rearrangement which confers an increased risk of miscarriage or live births with an unbalanced chromosome rearrangement. For couples ascertained following recurrent miscarriage, the risk of chromosomally unbalanced pregnancies surviving to term is low and therefore routine karyotyping of these couples is not indicated.

Referral information

From April 1st 2014, in accordance with the Royal College of Obstetricians and Gynaecologists guidelines, parental blood samples are no longer accepted from couples with isolated or recurrent pregnancy loss. Cytogenetic analysis may be performed on products of conception samples following the third and subsequent consecutive miscarriages or following the loss of a fetus with multiple structural abnormalities. Parental blood samples are accepted where: (1) testing of the products of conception sample shows an unbalanced structural fetal karyotype or (2) following the loss of a fetus with multiple congenital abnormalities or severe IUGR and material from the fetus or placenta is unavailable for cytogenetic testing.

View full test details for Recurrent Miscarriage

Introduction

Turner syndrome has a prevalence of approximately 1 in 2500 female births. In 50% of cases the syndrome results from the complete loss of one X chromosome in a female (a 45,X karyotype). Prenatally, Turner syndrome may present as cystic hygroma or fetal hydrops detected by ultrasound scan. Postnatally, the most common feature of Turner syndrome is short stature, which becomes evident by about age 5. The other main features include extra folds of skin on the neck (webbed neck), a low hairline at the back of the neck, puffiness or swelling (lymphoedema) of the hands and feet, heart problems, skeletal abnormalities, and/or kidney problems. Many affected girls do not undergo puberty unless they are treated with the hormone oestrogen. The majority of individuals with Turner syndrome are infertile, however, small percentage of females with Turner syndrome retain normal ovarian function through young adulthood. The majority of females with Turner syndrome have normal intelligence. Some Turner syndrome patients may have a cell line containing Y chromosome material which is associated with an increased risk of gonadoblastoma. In the majority of cases Turner syndrome arises as a sporadic event. Variant Turner syndrome can also occur when one normal X chromosome and one structurally abnormal X chromosome are present. Individuals with variant Turner syndrome may present with a milder phenotype than those females where a complete X chromosome is missing. Turner syndrome can also appear in a mosaic form, where normal cells are also present in the individual (a 45,X/46,XX karyotype). These individuals may exhibit a milder phenotype, which is dependent on the extent and tissue distribution of the normal cell line. One of the critical regions for the Turner syndrome phenotype, specifically short stature and skeletal abnormalities, is loss of the SHOX gene at Xp22.33.

Referral information

We accept prenatal samples (amniotic fluid and chorionic villus biopsies) from pregnancies where ultrasound scanning has shown a nuchal translucency measurement of greater than 3.5mm in the first trimester or 6mm in the second trimester, cystic hygroma or fetal hydrops. We accept postnatal blood samples from females with appropriate clinical features for a diagnosis of Turner syndrome. Tissue samples from pregnancy losses are also accepted.

View full test details for Turner Syndrome