FISHing in the Genomic Testing Age !

Genetic analysis has come a long way; we now have an ever-expanding collection of analytical tools in the diagnostic laboratory. So why do we still need a technique that usually only looks at one or two loci? The simple answer is that results from fluorescence in-situ hybridization (FISH) can quickly confirm diagnoses, guide clinicians’ judgements regarding differential diagnoses, and correlate results with clinical risk—thus enabling an informed choice of treatment type and intensity.

FISH employs fluorescently-labeled DNA probes to bind complementary DNA sequences within an interphase cell, or onto metaphase chromosomes. These sequences can then be visualized using fluorescent microscopy. The number, location and relative positions of the probe signals indicate chromosomal changes in a particular cell (Figure 1).

Many clinical trials use cytogenetic and FISH data to stratify patients according to specific risk factors. FISH is often used as a stand-alone technique for investigating abnormalities and following-up such patients, which, alongside its relatively low expense, makes it a very convenient investigative tool.

In this article we will explore the utility of FISH in today’s clinical laboratory and the future of the technique in the evolution of molecular testing.

Figure 1. The FISH process.

Figure 2. Interphase cell showing amplified HER2 signal pattern.

Read more: FISHing in the Genomic Testing Age !

Source: MedicalLaboratoryObserver

Download in PDF

Breast Cancer: The Body of Knowledge Grows

Scientists’ understanding of the genetics/genomics of breast cancer continues to grow; a revolution is underway both in terms of categorizing breast cancers and targeting treatment that will be effective in individual cases. New perspectives are being offered on the interpretation of biopsies, too. Here is a round-up of some very recent studies.

Genetic variants alter cells’ response to estrogen

An international study of almost 120,000 women has newly identified five genetic variants affecting risk of breast cancer, all of which are believed to influence how breast cells respond to the female sex hormone estrogen.

Estrogen acts as a trigger, binding to a molecule known as an estrogen receptor in most breast cells and triggering a cascade of signals that cause the cell to behave normally. However, the estrogen receptor is switched off in some cells and these do not respond to the hormone.

Read more: Breast Cancer: The Body of Knowledge Grows

Source: MedicalLaboratoryObserver

The Genetic Components of Rare Diseases

Techniques for determining which genes or genetic variants are truly detrimental

Last fall, the conclusion of the 1000 Genomes Project revealed 88 million variants in the human genome. What most of them mean for human health is unclear. Of the known associations between a genetic variant and disease, many are still tenuous at best. How can scientists determine which genes or genetic variants are truly detrimental?

Patients with rare diseases are often caught in the crosshairs of this uncertainty. By the time they have their genome, or portions of it, sequenced, they’ve endured countless physician visits and tests. Sequencing provides some hope for an answer, but the process of uncovering causal variants on which to build a treatment plan is still one of painstaking detective work with many false leads. Even variants that are known to be harmful show no effects in some individuals who harbor them, says Adrian Liston, a translational immunologist at the University of Leuven in Belgium who works on disease gene discovery.

Read more: The Genetic Components of Rare Diseases

CROSS COMPARE: Each model organism has its own vocabulary that researchers use to describe
an array of characteristics. The Monarch Initiative has mapped phenotype descriptions used in model
systems to human clinical features. The Initiative’s Exomiser software employs this mapping strategy
to help users better understand human genetic disorders by widening the pool of gene-function
associations. ROBINSON ET AL., GENOME RES, 24:340–48, 2014.

Source: the-scientist

Streamlining the E.coli Genetic Code

Scientists design a bacterial genome with only 57 codons.

The genetic code normally contains 64 codons, but researchers from Harvard University and their colleagues have designed an Escherichia coli genome with only 57 codons, replacing the others wholesale. In a paper published today (August 18) in Science, the team describes the computer-generated genome and reports on the first phases of its synthesis in the lab.

“We create something that really pushes the limit of genomes,” study coauthor Nili Ostrov, a postdoc in George Church’s lab at Harvard, told The Scientist. “The idea is that this is completely new, and we’re trying to see if it’s viable.”

In the planned 57-codon E. coli genome, each of the seven deleted codons is exchanged for a synonymous one.

Read more: Streamlining the E.coli Genetic Code

SCIENCE, CHRIS BICKEL

Source: the-scientist

A personal interpretation

There is a clear move away from a ‘one size fits all’ approach to medicine and instead a new personalized medicine strategy is becoming more important. Mike Furness explains more about multiomics.

It has been known for a while that people with different genotypes respond to drugs differently. Knowledge gained from studying rare genetic disease has improved understanding of important biological pathways, creating the opportunity for more effective treatments.

For early developmental diseases this has meant that each symptom is investigated in isolation, by a specialist in that area. The patient is sent from one clinician to another. On average a child with a rare genetic disease will been seen by seven physicians over a five year period before a diagnosis may be found. For many of these children there will be no diagnosis but recent advances in genomics will address this problem.

It was against this background that the Discovering Development Disease (DDD) project was established between the NHS and the Wellcome Trust Sanger Institute. It has so far genotyped around 14,000 children with undiagnosed conditions and their parents, providing diagnoses for around 40% of these families, and identifying clusters of affected children that had similar clinical characteristics and shared damaging genetic variants in the same gene. Many of these genetic diseases are so rare that a clinician may see only one or two cases in a career; so being able to compare their patient’s genetics to this growing body of knowledge is a major step forward in helping consultants determine a definitive diagnosis.

Read more: A personal interpretation

Source: shutterstock

Recent Progress in Genome Editing

Researchers develop a CRISPR-based technique that efficiently corrects point mutations without cleaving DNA.

Most genetic diseases in humans are caused by point mutations—single base errors in the DNA sequence. However, current genome-editing methods cannot efficiently correct these mutations in cells, and often cause random nucleotide insertions or deletions (indels) as a byproduct. Now, researchers at Harvard University have modified CRISPR/Cas9 technology to get around these problems, creating a new “base editor,” described today (April 20) in Nature, which permanently and efficiently converts cytosine (C) to uracil (U) bases with low error in human and mouse cell lines.

“There are a lot of genetic diseases where you would want, in essence, to swap bases in and out,” said Jacob Corn, scientific director of the Innovative Genomics Initiative at the University of California, Berkeley, who was not involved in the research. “Trying to get this to work is one of the big challenges in the field, and I think this is a really exciting approach.”

Read more: Recent Progress in Genome Editing

Illustration of DNA ligase, one of the cell proteins involved in repairing double-strand breaks in
DNAWIKIMEDIA; WASHINGTON UNIVERSITY SCHOOL OF MEDICINE IN ST. LOUIS

Source: wikimedia