Phenotypes

• Linkage analysis


  Why do we want to know which of the informative meiosis in a pedigree is recombinant or non-recombinant?
• Recombination rate

  • Markers
  • The "disease gene" must be around here
• Linkage analysis: Logarithm of Odds

  i.e., Genetic distance between the marker and the disease gene
• Two-point linkage analysis


  • Linkage analysis
  • LOD scores plotted against recombination fraction
• Z ≥ 3 is significant for linkage. Z < −2 is significant against linkage.
• Finding disease genes using genetic linkage and high-throughput sequencing


  1. Collect multi-case, multi-generation family/families

  2. Linkage analysis

  3. Local gene list, prioritisation

  4. Candidate gene sequencing, segregation analysis
• Finding disease genes by exome/genome sequencing

  1. Collect multi-case and/or several core families

  2. Long list of variants in different locations

  3. Shortlist of candidate variants

  4. High-throughput sequencing

  5. Gene list, filtering, prioritisation

  6. Segregation analysis, independent cases
• Exome sequencing can be used to find disease genes for facial abnormalities, missing fingers/toes, frequent mosaicism, extremely rare disease (approximately 1 case per 1 million newborns)
• Mode of inheritance?

  Miller syndrome
• Exome sequencing: Filter

  1. 2 affected sibs

  2. Genetic model (dominant, recessive)

  3. Mutation type

  4. Databases

  5. Prediction
• DHODH (dihydroorotate dehydrogenase) is the gene found to cause Miller syndrome
• Mutation types

  • Missense
  • Insertion & deletion
  • Silent
  • Splice site
  • Nonsense
  • Dynamic
• Dynamic mutations

  Can occur by extension of short 'tandem' repeats. Above a certain size, these sequences become unstable. Dynamic mutations in UTR or coding sequences can be associated with disease.
• Examples of diseases caused by dynamic mutations

  • Fragile X syndrome (FMR1)
  • Myotonic dystrophy (DMPK)
  • Huntington disease (HTT)
  • Spinocerebellar ataxia 1 (ATXN1)
  • Synpolydactyly 1 (HOXD13)
• Huntington disease is caused by CAG repeat expansion in the gene HTT, which codes for huntingtin. The mutant huntingtin has an expanded poly-glutamine tract and forms protein aggregates, which do not promote secretion of neurotransmitters and lead to apoptosis.
• Propensity for somatic expansion of CAG repeats increases over the course of life in Huntington disease
• Anticipation

  Occurs when a disease manifests earlier and/or increases severity with successive generations. Anticipation is suspected when a mild disorder is observed in a parent/relative after diagnosis in the child/index patient.
• Fragile X syndrome is an important example for diseases that show anticipation.
• Loss of function

  Mutations are mainly recessive. For some genes, product amounts from one copy instead of two are not sufficient, leading to haploinsufficiency. Mutations causing haploinsufficiency are usually dominant.
• Gain of function

  Can be associated with gross overexpression of certain genes, acquisition of a novel function and production of chimeric genes, modification of cellular signalling responses.
• Diseases caused by gain of function mutations


  • Charcot-Marie-Tooth disease 1A (PMP22)
  • Albright syndrome (GNAS)
  • AML (GSTP1)
  • Hypokalemic periodic paralysis (SCN4A)
  • Osteogenesis imperfecta (COL1A1/A2)
  • Chronic myeloid leukemia (BCR-ABL)
• Chronic myeloid leukemia is caused by a translocation between chromosomes 9 and 22 resulting in a fusion gene BCR-ABL1, which encodes a constitutively active tyrosine kinase.
• Protein aggregation

  Changes in the physical surface properties can result in protein aggregation, as seen in sickle cell anemia.
• Protein misfolding

  Mutations in genes for connective tissue proteins such as collagens can explain normal protein assembly and disease mechanisms caused by protein misfolding.
• Type I collagen biosynthesis

  Collagen type I consists of two α1-chains and one α2-chain. These chains have to align in order to start the folding process of procollagen type I into a triple helix. After this folding process, post-translational modifications and collagen trimming by specific proteins have to take place.
• Protein dimers

  Mutations can lead to mild disease by loss of interaction or severe disease by dominant negative activity.
• Osteogenesis imperfecta (OI) can be caused by mutations in COL1A1 and COL1A2 (and several other genes). The severity of the disease depends on the type and position of the mutation.
• Genotype/phenotype correlation in Osteogenesis imperfecta

  Dominant negative mutations that impair the coordinated assembly of collagen fibers explain the strong genotype/phenotype correlation. Mutations in N-terminal domains lead to milder diseases than mutations in C-terminal domains.
• Types of genetic diseases

  • Monogenic (Mendelian)
  • Polygenic
  • Multifactorial
• Polygenic inheritance

  Variants contributing to the disease, threshold for being clinically affected
• Multifactorial diseases

  Combinations of genetic and environmental factors
• Most diseases are caused by the combined effects of multiple genes and environmental factors