Topic 10: giant case study

Question 1

why is height a complex trait?

Answer 1

includes many bioligcal and environmental factors

Question 2

what are the biological factors of height?

Answer 2

• pathogenesis often involves several tissues (pituitary, liver, bones, growth plate)
• signalling pathways have many members (thyroid hormone, growth hormone)
• effects of genetic changes may be buffered (growth potential, catch-up growth)

Question 3

what are the environemntal factors of height?

Answer 3

• many influences (infections, protein malnutrition, socio-economic factors)
• exposure often hard to measure (many are not even known)
• effect of exposure differs with age (infant v. adolescent v. adult)

Question 4

how does the heratibility of height differ between infants and adolescents?

Answer 4

infant: 0.2-0.5
adolescent: 0.7-0.9

Question 5

how is growth assessed in clinic?

Answer 5

using growth charts that take into accoutn the height of the mother and the father to get an estimate of what the child’s height should be, with the middle line being the 50th percentile and going from 97th to 3rd percentile which would still tehcnically be considered normal, as long as the child stays within the same line throughout development

Question 6

what is catch-up growth?

Answer 6

when a child has some sort of abnormaility with its growth but then you change something/fix something and the child then quickly goes back to its normal growth trajectory

Question 7

protein malnutrion leads to ______

Answer 7

irreversibel growth retardation, where you can never “take back those inches” even if they go back to eating properly

Question 8

what does improper body proportions in child with stunted growth hint at?

Answer 8

problem with thyroid (hypothyroidism leading to goider)

Question 9

what are the broad classifications of bone/growth disorders?

Answer 9

1. epiphyseal abnormility (small secondary epiphyseal)
2. metaphyseal abnormality ( unequal metaphysis edge)
3. diaphyseal abnormaity ( bigger diaphysis)
4. spnodylo-abnormalitiy (smaller vertabrae)

Question 10

what key features can be seen on a hand and leg x-ray of a person with achondroplasia?

Answer 10

• small hand (generally looks like that of a 8 yr old)
• immature epipheaseal plate at the wrist
• in leg, no clear seperation bwn epiphysis and growth plate

Question 11

how are the body proportions in a person with achondroplasia?

in legs specifically

Answer 11

shorter thigh than leg

Question 12

what is the genetic cause of achondroplasia?

Answer 12

mutation of FGFR3, leading to a gain of function in the growth plates (constitutive activation)

Question 13

what symptoms are seen in a person with achondroplasia?

Answer 13

• obesity, sleep apnea, recurrent ear infections
• spinal curvature, bowed legs, arthritis
• narrowing of lower spinal canal (spinal stenosis)

Question 14

can achondroplasia be inherited?

Answer 14

80% de novo, 20% inherited

Question 15

what does FGF3R do?

and what happen when it is mutated?

Answer 15

it is a receptor tyrosine kinase that leads to activation of the MAPK pathway, leading to chondrocyte differentitation, and activation of STAT, leading to inhibition if chorndrocyte proliferation

Question 16

what is the most common mutation in FGF3R?

Answer 16

Gly380Arg (in TM domain)

Question 17

what does Vosoritide do?

Answer 17

it is a c-type natriuretic peptide that inhibits FGFR3 downstream of signalling (at level of Raf1), stimulating chorndrocyte proliferation and differentiation.

for achondroplasia

Question 18

what vosoritide showed to work in its clinical trial?

Answer 18

yes, and when they saw such a big difference between placebo and therapy, they began giving the therapy to the placebo group where they saw big improvment like seen in the other group.

Question 19

what is the genetic cause of Morqio A syndrome?

Answer 19

N-acetylgalactosamine 6-sulfatase (AR) (GALNS)

Question 20

what can be seen in x-rays of a person with Moroqio A syndrome?

Answer 20

• fish-shaped and light/weak spin
• in hand, disorganized epiphyseal plates at bottom of hands and no wrost bones/no epiphysis

Question 21

what does GALNS do?

Answer 21

removes sulfate from keratan sulfate, where deficiency leads to accumulation of keratan sulfate in lysosomes

Question 22

what symptoms and features are seen in patients with Morquio A syndrome?

Answer 22

• enlarged skull, platyspondyly and dorsolumbar kyphosis
• epiphyseal irregularity, widened metaphyses
• cloudy cornea, thin tooth enamel, multiple cavities, heart valve abnormalities, mild liver enlargement
• atlanto-axial instability (hypoplasia of odontoid process)
• joint pain, early onset arthritis

Question 23

what does Vimizim therapy do?

Answer 23

IV infusion to relapce GALNS, leading to sustained imporvemtn in distance walked

Question 24

what x-ray features can be seen in people who have multiple epiphyseal dysplasia?

Answer 24

immature wrist bones and problems in the hip

Question 25

what is the genetic cause of multiple epiphyseal dysplasia?

Answer 25

COMP (catilage oligomeric matrix protein), which normally activates TGF-BR, which when mutated leads to lack of proliferation/differentiation of chorndrocytes and structural integrity of cartilage/tendons/ligaments | so similar to achondroplasia but worse

Question 26

what can be seen on the x-rays of a personw ith Osteogenesis Imperfecta Type 1?

Answer 26

multiple healing fractures

Question 27

what is the genetic cause of osteogenesis imperfecta type 1?

Answer 27

COL1A1, leading to defects in type 1 collagen synthesis, processing, transport

Question 28

what are symptoms of osteogenesis imperfecta type 1?

Answer 28

- bone fracture after minor trauma - bowing of legs + pther deformities - short strature

Question 29

what is the recombination rule of thumb? | families

Answer 29

* Typically, one recombination event occurs in each chromosome arm per generation * Two loci that are 1 centimorgan (cM) apart have a 1% chance of being separated by recombination in a single generation (1cM is about 1 million bases)

Question 30

what is the recombination rule of thumb? | populations

Answer 30

* Recombination often occurs in the same small region of the genome (“hotspots”) * Results from chromatin structure and specific “fragile” DNA sequences (trinucleotide repeats)

Question 31

what is the rationale for tag SNP-based association studies?

Answer 31

- statistical tests detect association (not causation) - SNPs may be genetically indistinguishable or "linked" to each other as a result of biological processes

Question 32

what is a key consideration when doing population studies?

Answer 32

need to make sure cultural origins are the same between all groups that are being testing in order to make sure that the genetic differences seen are due to disease and not place of origin

Question 33

what are the different disease association statistical tests/models?

Answer 33

* additional * dominant * recessive

Question 34

what are trait association studies done in GWAS?

Answer 34

modelled using linear regression can determine effect (slope of line) from background noise (correlation) and report significance of association (P-value) | only significant when above the line (smaller p-value than normal)

Question 35

what gene was associated with adult height (GWAS)? | european origin

Answer 35

**HMGA2** is a non-histone chromosomal high-mobility group (HMG) protein

Question 36

what did the GIANT consortium find? | Genetic Investigation of ANthropometric Traits

Answer 36

* 83 SNPs in coding * rest in non-coding * most located in or near: GH, GHR, IGF1, ... * many genes regulating skeletal developemnt (TGF-b, hedgehog), chondrocyte development, and extracellualr matrix formation

Question 37

what types of genes are generally found in GWAS studies?

Answer 37

generally genes that may be more common and have smaller effect size.

Question 38

what type of study is used to find rare coding SNPs with high effect size, uncommon coding SNP with modest effects, and common SNPs with low effect size?

Answer 38

- rare: linkage studies - uncommon: whole exome sequencing - common: GWAS or whole exome sequencing

Question 39

what is the first step in interpretating a GWAS study? | and how can it be done

Answer 39

First steps include discovering which types of cells have enhancers or promoter that contain the SNP and then seeing whether the SNP affects expression of nearby genes – this can be done using collections of tissues collected from different people (GTeX Consortium)

Question 40

why is it that association studies have multiple testing?

Answer 40

since genotyping platforms perform hundreds of thousands of independent tests, significance threshold is reduced to avoid making a false discovery (Type I errors)

Question 41

what is allelic spectrum?

Answer 41

describes relationship between effect size and allele frequency of associated variants, and can alos consider functional properties of effector alleles (coding vs non-coding) | `

Question 42

what genes are associated with BMI?

Answer 42

FTO

Question 43

how do we interpret GWAS studies?

Answer 43

- first find where the gene is expressed - then do functional assessments

Question 44

what is genetic fine mapping?

Answer 44

in GWAS, we get a noisy result where it is hard to find the true "signal," meaning that the true signal may be missed. Then fine mapping allows us to find the actual causative variants, reducing the number of SNPs that cna be used for functional studies

Question 45

why use fine-maping in a GWAS study?

Answer 45

1. to find causal genes (effector transcripts) -- causative coding variants/regulatory variants 2. to link variant with a functional or regulatory pathway -- experimental validation, disease pathogenesis 3. to understand genetic architecture -- type of variant, compare across traits/populations, devlop models

Question 46

what is a conditional analysis in GWAS?

Answer 46

condition on a lead SNP and test whether there are any other SNPs that remain significantly associated

Question 47

what did a conditional analysis for BMI allow us to find?

Answer 47

secondary signals in MC4R

Question 48

what are the challenges in identifying causal variants in a trait-associated locus?

Answer 48

* the variant (SNP) with the strongest statistical association in the region is frequently (usually) not the causal variant * most approaches search for a single causal variant; however, the phenotype may result from the combined effects of several variants * regions in tight linkage disequilibrium (LD) are often inherited as haplotype blocks without recombination – so the study population does not have sufficient combinatorial complexity to dissect the effects of individual variants

Question 49

what are some considerations when selecting the best candidates in GWAS studies?

Answer 49

based on convergence of actual or predicted effects of genetic variants: coding variant, variants in regulatory elements

Question 50

what does colocalization tests tell us?

Answer 50

tests whether genetic associations of two traits at a specific locus are explained by the same variants or distinct variants

Question 51

what do eQTLs tell us? | Expression quantitative trait loci

Answer 51

link SNPs to genes

Question 52

what are 3 situations that can lead to this transcriptional change to phenotype seen?

Answer 52

can be either causality: causal variant to transcription to phenotype pleiotropy: causal variant leading to both transcriptional change and phenotype linkage: causal variant 1 leading to transcriptional change which is linked to another causal variant which leads to phenotype

Question 53

what is the massivley parallel reporter assay (MPRA) workflow?

Answer 53

it measures the effect of thousands of variants on transcriptional (enhancer) activity in the lab: region selection, barcode amplication, analyze fequncy of candidates

Question 54

what does FTO do?

Answer 54

2-oxyglutarate and Fe(II) dependent nucleic acid demethylase (DNA & RNA)

Question 55

which type of fat does FTO generally affect?

Answer 55

predominantly effects subcutaneous fat (not visceral fat or fat distribution)

Question 56

what does FTO loss of function lead to?

Answer 56

syndrome with postnatal growth retardation, microcephaly, severe psychomotor delay, and death before age 30 months

Question 57

what are the steps n a study aimed at identofying a mechanistic basis for the association between the FTO locus and obesity in humans?

Answer 57

1. Step 1: Identify potential regulatory elements and target cell types 2. Step 2: Identify candidate effector transcripts in chromatin region 3. Step 3: Assess gene expression in people carrying the risk variant 4. Step 4: Demonstrate link between candidate effector transcript and adipocyte differentiation and function 5. Step 5a. Study effects of lead variant on gene expression (I) (establish whether it changes effector gene expression) 6. Step 5b. Study effects of lead variant on gene expression (II) (establish whether it changes adipocyte function)