Pediatric Nephrology

, Volume 27, Issue 6, pp 873–883 | Cite as

Genetic testing in renal disease

  • Detlef Bockenhauer
  • Alan J. Medlar
  • Emma Ashton
  • Robert Kleta
  • Nick Lench
Review

Abstract

A revolution is happening in genetics! The decoding of the first genome in 2003 was a large international collaborative effort that took about 13 years at a cost of around $2.7 billion. Now, only a few years later, new technology allows the sequencing of an entire genome within a few weeks—and at a cost of less than $10,000. The vaunted $1000 genome is within reach. These extraordinary advances will undoubtedly transform the way we practice medicine. But, like any new technology, it carries risks, as well as benefits. As physicians, we need to understand the implications in order to best utilise these advances for our patients and to provide informed advice. In this review, our aim is to explain these new technologies, to separate the hype from the reality and to address some of the resulting questions and implications. The practical objective is to provide a simple overview of the available technologies and of purpose to which they are best suited.

Keywords

Kidney Inherited disease Genetic testing Next-generation sequencing Genome Exome 

Notes

Glossary

Allele

refers to forms of DNA sequence. A SNP typically has two alleles: A vs. T or C vs. G. A gene can have many alleles, defined by several sequence variations within the sequence of the gene. In early genetics, allele referred to a variant of a gene that resulted in a certain phenotype, such as eye colour or blood group.

Amplicon

a stretch of DNA defined by the location of the two olgonucleotide primers used in the PCR. The stretch of DNA flanked by the primers will be amplified by PCR.

Compound heterozygous

refers to a situation in a recessive diseases, where the mutation found on one allele is different from that found on the other allele.

Exome

refers to the stretches of DNA in the genome that are actually protein-coding. It makes up only about 1% of the entire genome, but harbours approximately 85% of all disease-causing mutations. Whole-exome sequencing is becoming increasingly common for the identification of mutations in rare single-gene disorders, but is likely to be replaced by whole genome sequencing in the future.

Genotype

the genetic makeup of an individual. This can refer to a single nucleotide variation (e.g. A vs. T or C vs. G) or the combination of many such variations, for instance as determined by a SNP array.

Homozygous

if the two alleles in an individual are identical by descent. This can be for a single nucleotide (e.g. a SNP) or larger stretches of DNA (e.g. a gene).

Heterozygous

if the two alleles in an individual are different.

Linkage

describes the tendency of two loci to be inherited (linked) together when assessed across generations of a family. Loci in close physical proximity tend to be inherited together. Two loci are considered linked if they are co-inherited more often than by chance alone.

Linkage disequilibrium

describes the tendency of alleles to be inherited together when assessed across the population. It describes the difference between the observed allelic frequencies and what we would expect given truly random inheritance. The more commonly two alleles are inherited together, the stronger they are in linkage disequilibrium. In contrast to linkage, which reflects physical proximity only, linkage disequilibrium can also reflect other factors. For instance, two genes on separate chromosomes can be in linkage disequilibrium if they are functionally interdependent and evolved under the same constraints.

Locus

a physical location on a chromosome of a gene or DNA sequence.

Missense mutation

a mutation that results in a change of the encoded amino acid; for example, from lysine to threonine.

Nonsense mutation

a mutation that results in a premature stop codon.

Re-sequencing

refers to the multiple sequencing of individual DNA fragments common in next-generation sequencing. In contrast to conventional (Sanger) DNA sequencing, where each stretch of DNA is sequenced only once.

Risk allele

the allele of a SNP that is associated with a given disease. Genome-wide association studies investigate which form of a SNP (e.g. A or T) is associated with the disease. The associated form is called the risk allele.

SNP

single ucleotide polymorphism. Variation of a single nucleotide in the genome. SNPs are typically considered non-pathogenic and by definition have a frequency of >1% in the general population.

SNP array

a microarray or chip to determine the genotype of many SNP simultaneously. SNP arrays vary in size and may contain between 10,000 to >1,000,000 SNPs.

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Copyright information

© IPNA 2011

Authors and Affiliations

  • Detlef Bockenhauer
    • 1
    • 2
    • 4
  • Alan J. Medlar
    • 2
  • Emma Ashton
    • 3
  • Robert Kleta
    • 1
    • 2
  • Nick Lench
    • 3
  1. 1.Institute of Child HealthUniversity College LondonLondonUK
  2. 2.Centre for NephrologyUniversity College LondonLondonUK
  3. 3.North East Thames Regional Genetics Service LaboratoriesGreat Ormond Street Hospital for Children NHS TrustLondonUK
  4. 4.Great Ormond Street Hospital for Children NHS TrustLondonUK

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