Limitations of tests

Different sample types yield cytogenetic preparations with different G band resolutions, with blood samples giving the highest resolution. An abnormality could be detected in a blood sample but not in a prenatal  sample from the same patient. Since the expected resolution varies between sample types, a case may be reported as substandard on a blood sample and still have been analysed at a higher resolution than from a different sample type from the same patient. If the minimum banding resolution recommended by national professional standards is not met, this will be stated in the report.

Mosaicism (the presence of two or more populations of cells with different karyotypes in one individual) may not be excluded by routine karyotyping. If there is an indication of mosaicism, additional cells will be examined to exclude a 10% level of mosaicism at a 95% confidence level. This will not exclude mosaicism in other tissues.

Cytogenetic analysis cannot fully exclude mosaicism, or very small structural chromosome abnormalities. If mosaicism is suspected, the number of cells examined will be increased to improve the probability of detection of low level mosaicism.

Blood samples from parents or other family members (collected in lithium heparin tubes) or an additional sample from the same patient may be required to interpret the cytogenetic result. If required, samples will be requested in the report or, where the test is urgent, in discussions with the referring department.

Our standard resolution of preparations for karyotype analysis from blood samples will detect most abnormalities larger than 5Mb. The laboratory adheres to national professional standards for the minimum acceptable resolution for specified reasons for clinical referral. A repeat sample may be requested if the minimum quality standards are not met.

FISH can only detect deletions or duplications of regions specifically targeted by the probe used and which are the same size or larger than the probe used. Smaller deletions or duplications may not be detected.

Data generated by the Infinium Global Screening Array-24 Kit platform and analysis performed at a genome-wide resolution of 200kb using Nexus Clinical v6.1 software (GRCh38).

This test will not detect balanced rearrangements or single nucleotide variants and may not detect all cases of mosaicism or copy number variation in regions with high sequence similarity to other regions of the genome. This test will not detect certain forms of uniparental disomy without parental samples and does not show genomic position or orientation of copy number gains. Genomic coordinates are approximate according to the limitations of the array platform.

Classification of copy number variants is according to ACMG and ACGS guidelines and is based on evidence available at the time of analysis. Classification may change with new evidence or guidelines. Copy number variants of uncertain clinical significance will not be reported unless additional testing may provide evidence for pathogenicity. Carrier status for recessive disorders will not be reported. Regions of Homozygosity of autosomes ≥10Mb and clinically significant regions of Uniparental Isodisomy ≥10Mb will be reported. Reporting of incidental findings will be according to BSGM Incidental Findings guidance and local policies.

Mosaicism may be difficult to interpret when detected in a prenatal sample. Confined placental mosaicism is observed in approximately 1-2% of chorionic villi samples and further invasive testing may be required to interpret these cases.

In cases where the minimum G-banding analysis resolution recommended by national professional standards has not been achieved, this will be stated in the reports.

There is a small risk of overgrowth of maternal cells in amniotic fluid or chorionic villi long term cultures.

Blood samples from parents may be required to clarify the cytogenetic result. If required, these samples will be requested in discussions with the referring department.

Prenatal karyotype analysis is carried out on long term cell cultures. Targeted chromosome analysis is performed in cases where aneuploidy has been detected by QF-PCR to exclude a chromosome rearrangement which may have been inherited and have a recurrence risk. This cannot exclude mosaicism, or subtle structural chromosome abnormalities. If mosaicism is suspected the number of cells examined will be increased to improve the probability of detection of low-level mosaicism.

Data generated by the Infinium Global Screening Array-24 Kit platform and analysis performed at a genome-wide resolution of 200kb using Nexus Clinical v6.1 software (GRCh38).

This test will not detect balanced rearrangements or single nucleotide variants and may not detect all cases of mosaicism or copy number variation in regions with high sequence similarity to other regions of the genome. This test will not detect certain forms of uniparental disomy without parental samples and does not show genomic position or orientation of copy number gains. Genomic coordinates are approximate according to the limitations of the array platform.

Maternal cell contamination may be detected by an array test and may result in the array test being non reportable.

Classification of copy number variants is according to ACMG¹ and ACGS² guidelines and is based on evidence available at the time of analysis. Classification may change with new evidence or guidelines. Copy number variants of uncertain clinical significance will not be reported unless additional testing may provide evidence for pathogenicity. Carrier status for recessive disorders will not be reported. Regions of Homozygosity of autosomes ≥10Mb and clinically significant regions of Uniparental Isodisomy ≥10Mb will be reported. Reporting of incidental findings will be according to BSGM Incidental Findings guidance³ and local policies.

 

DNA extracted from products of conception, skin and placenta biopsies is analysed by the Infinium Global Screening Array-24 Kit platform which will detect most genetic causes of miscarriage including aneuploidy, triploidy and complete molar pregnancies. Maternal contamination cannot be excluded in productions of conception and placental samples when a normal female result is obtained. 

This test will not detect balanced rearrangements or single nucleotide variants and may not detect all cases of mosaicism or copy number variation in regions with high sequence similarity to other regions of the genome. This test will not detect certain forms of uniparental disomy without parental samples and does not show genomic position or orientation of copy number gains. Genomic coordinates are approximate according to the limitations of the array platform.

Classification of copy number variants is according to ACMG and ACGS guidelines and is based on evidence available at the time of analysis. Classification may change with new evidence or guidelines. Copy number variants of uncertain clinical significance will not be reported unless additional testing may provide evidence for pathogenicity. Carrier status for recessive disorders will not be reported. Regions of Homozygosity of autosomes ≥10Mb and clinically significant regions of Uniparental Isodisomy ≥10Mb will be reported. Reporting of incidental findings will be according to BSGM Incidental Findings guidance and local policies.

Karyotype provides a genome wide screen, albeit at a low resolution. If the size of the malignant clone is small, the cells analysed may be normal, because the abnormal clone is not represented.

This test cannot be used for MRD monitoring.

The quality of G-Banded cells for karyotype, particularly for the malignant cells, may be poor and small abnormalities may not be detected.

A normal karyotype result does not necessarily exclude a clonal cytogenetic abnormality.

Karyotype will not detect small DNA sequence variants. DNA based tests may be more suitable in some cases.

FISH is a targeted test which will only give an answer to a specific question. Low level clones may not be detected.

If the size of a malignant clone is small, the cells analysed may be normal. Variant FISH patterns may be more difficult to interpret.

FISH will not detect all gene rearrangements, e.g. micro insertions into a gene of interest may not be detected. Break apart probes cannot identify the partner gene and RNA fusion testing may be recommended.

A false positive FISH result is possible, if a gene close to the target and also covered by the FISH probe, is rearranged.

For paraffin embedded tissue sections, truncation of nuclei may make interpretation difficult. Screening for deletions is not typically recommended on tissue sections, where it is carried out a deletion will not be reported unless the clone is large.

For paraffin sections we require a marked H+E slide in order to target our analysis to the abnormal cells. Alternatively, a statement may be provided that all tissue is representative. Percentage tumour load will aid interpretation.

FISH will not detect small DNA sequence variants.

FISH testing on interphase cells may produce a different result from karyotype, because karyotype specifically targets the population of cells that is actively dividing. FISH analysis provides a non-selective screen of the cell population.

Microarray is a genome wide screen. Analysis is carried out at 5 Mb resolution with a higher resolution analysis of disease-specific target genes.

This test will not detect balanced rearrangements or point mutations and may not detect low level clones. Since this test uses total sample DNA clonal architecture cannot be determined.