Lecture 7 Flashcards
what are some traits of second generation sequencing?
- 10,000 fold drop in the cost of sequencing since 2005
- for typical geneticist needs, only exome sequencing is required
- 160,000 exons is the selective coverage
- newer kits also include 3’ and 5’ UTRs
what is the degree of deep sequencing needed when we expect mutations in only in some but not all of sequence reads?
5000X targeted sequencing
what is a detailed comparision between WGS and targeted panels?
WGS-most expensive and time costly
-targeted panels-almost evens out by cost with WES
what happens in next generation DNA sequencing
- targeted gene panel
- whole exome sequencing
- whole genome sequencing
what are the steps in bioinformatics analysis?
- variant identification
- exclude synonymous mutations and polymorphisms
- prioritize variants using the assumed inheritance pattern of the disease
- in silico predication of variant effects
- identify previously reported mutations associated with human disease
- prioritize novel mutations using existing knowledge of gene function
what are the parts of functional validation?
- protein expression
- protein function in cells
- animal models of disease
what is antenatal bartter syndrome?
- mutations in NKCC2, ROMK, or Barttin
- severe phenotypes
- lab: hypercalciruia and high urinary [Cl-]
- nephrocalcinosis may manifest later in life
what is classic bartter syndrome
- mutations of CIC-K
- develop normally during the first 2-5 years of life
- BP is low normal
- lab: hypercalciuria and higher urinary [CL-]
- nephrocalcinosis is usually absent
what happened when researchers sequenced only the exome, the most important parts in suspected Bartter syndrome patient, a renal salt wasting disease?
they discovered a congenital chloride diarrhea instead, homozygous mutation in SLC26A3
is CCD found by mistake when sequencing the exome for bartter syndrome a treatable disease?
yes, aggressive salt replacement therapy is needed
what is the strategy when you have 4 unrelated individuals with Freeman–Sheldon syndrome (FSS) and
8 healthy individuals from 3 different populations for exome sequencing?
find variations common for FSS but absent in controls
what is the common variation exome sequencing found for FSS?
MYH3 mutation (heavy myosin 3)
what are the symptoms associated with freeman sheldon syndrome FSS?
- artogriposis
- clubfoot due to contracture
- severe face defects
- scoliosis
what are the symptoms of sheldon hall syndrome?
- artrogriposis
- clubfoot due to contracture
- severe face defects rare
- scoliosis rare
- calcaneovalgus
how did exome sequencing help with Miller syndrome?
from 4 infected individuals from 3 families, ex sequencing found 2 different mutations in DHODH gene, it was then confirmed by regular DHODH sequencing in 3 other families
how are Nager and MIller syndrome similar?
symptoms of miller are: missing pinkies, facial features, automosomal recessive
symptoms of Nager are: missing thumbs, facial features, autosomal recessive or dominant. Hoped mutations would be caused on some unknown gene but resequencing of Nager showed no DHODH mutation
what are the symptoms of primary ciliary dyskinesia?
lots of bronchitis, headaches, infertility
what are the symptoms of Charcot-Marie Tooth Neuropathy
- digital sensory loss and weakness (especially on cold exposure)
- deep tendon reflex abnormalities
- sometimes skeletal deformities
what are some of the issues with whole genome sequencing for personalized medicine and for clinical diagnostics?
- error rates, quality scores
- data storage, computational power
- up front database management
- assembling the genome
true or false: 23 and me is an example of exome sequencing
false!!!! 23 and me is not exome sequencing, chip based genotyping
what is genotyping described as?
refers to sampling specific known positions in the genome of interest, known to vary between the populations or be associated with certain traits/diseases
what are the traits of genotyping?
- returns information on genetic variants you know about
- will not question more variants than you originally designed the chip for
- cheaper than sequencing
what are the ACMG guidelines for clinicians as it pertains to ordering tests?
- released a minimum list of incidental findings to report
- disorders where prevention and/or treatment are available and where individuals with pathogenic mutations might be asymptomatic for long periods of time
- only variants that met pathogenic criteria
- responsibility for managing incidental findings is placed on the ordering clinician
- labs will bear increased burden of added analysis and confirmation of variants
what are some recent advances thanks to whole genome sequencing
- 50 hour differential diagnosis
- intended to be a prototype for use in neonatal intensive care units (examples are severe GJB2 related skin disease and BRAT1 related lethal neonatal rigidity and multifocal seizure syndrome in another infant)
what is a key feature in WGS advances
sequencing of parents or affected siblings expedites the identification of disease genes in prospective cases
what are CNV’s (copy number variants) associated with?
major cause of complex diseases, represent a novel independent cause of genetic morbidity for neurogenetic disorders
what are some of the illnesses associated with CNV’s (copy number variants)?
- intellectual disability
- autism and ASD
- epilepsy
what are the ways to detect CNV (copy number variants)?
mapped reads and paired reads
what is penetrance?
probability of developing a particular disease given a particular genotype
what is age dependent penetrance?
so percentage of people with the genotype developing the disease by age 40, by age 50 and so on
what is lifetime risk?
probability that you ever develop the disease before you die. Lifetime risk can never quite be 100%, because you could always die of something else first
fill in the blanks: completely penetrant genetic (1)_______ should not be more common in the (2) ________ than the (3) ________ that it causes
(1) variant
(2) population
(3)disease
Completely penetrant genetic variant should not be more common in the population than the disease that it causes
what is todays biggest limitation with WGS?
sample size
what is the law on sequencing?
it can only be on order of a physician
what are the newborn symptoms of antenatal bartter syndrome?
-newborn symptoms: hypokalemia, metabolic alkolosis, vomiting and failure to thrive, history of polyhydramnios and premature delivery, polyuria
what are symptoms of classic bartter syndrome?
- vomiting, polyuria, recurrent episodes of dehydration, and fever
- carpopedal spasms and fatigue
- many children show developmental delay
