What do you think of when you here the word genome?

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Tyler Lucas
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1 What do you think of when you here the word genome?

2 What do you think of when you here the word genome?

3 Personal Genomics Outline Review of pre-lab work Genomics and Medicine Case Overview & Assignment Groups will work on case Present case

4 How would this protein migration change with these mutations? Base Substitution Missense mutation Nonsense mutation Silent mutation Neutral mutation Insertion or Deletion Downstream nonsense mutation Triplet Insertion

5 What information about the mutation will a western blot provide? Assume you have a variety of antibodies. Base Substitution Missense mutation Nonsense mutation Silent mutation Neutral mutation Insertion or Deletion Downstream nonsense mutation Triplet Insertion

02 - aspartic acid is 3.02 - lysine is 9.

6 What information about the mutation will a 2D gel provide? Isoelectric Point (IP) is the ph where the protein (or amino acid) charge is 0. - alanine is aspartic acid is lysine is 9.74 If the previous two slides indicate a protein of the same size what will a 2D gel tell us? What mutation would cause: a) The spot to move to left but same on the SDS page? b) The spot to move to right but same on SDS page?

7 Genome Sequences Technology of the 21 st Centruy Genome (partial) sequences are cheaper and easier to get for the general public. 23 and me is one example What are some benefits and concernts with this kind of technology? Lets look at some data from 23 and me

8 Lets consider some cases with a 23 and Me patient During a routine visit a patient revels they are quite worried about some results they just received from 23 and me. You look at her/his data which include: The portion of the gene that is mutated (only the template strand without introns). You will look at your patients gene sequence for both of their alleles and compare it with a normal gene sequence Does it have a mutation? How would you characterize this mutation? What will the result be to the final protein? How will this protein appear on a SDS-PAGE, Western (with N-terminal and C- terminal antibody), and a 2D gel For this draw what the gel looks like compared to normal gene. Determine the risk of this patient getting this disease What would you advise this patient to do to reduce their risk? Determine the risk of the patient passing this disease on (in a general sense) What choices does this patient have?

9 Patient 1 Ethnicity: African American male Age: 45 years old Health: Appendectomy at age 10, suffers from asthma, and tires easily. Family history: Ancestors are from Nigeria; father had a heart attack at age 65 and is still living (age 77). His mom is alive and is 72 years old. Grandfather died of myocardial infarction at age 55. Several distant relatives died at an early age but there were poor medical records. Gene of interest from 23andMe: HBB HBB gene: 441 nucleotides (without introns); codes for 147 amino acids; KDa Partial Normal sequence: Patient Allele Sequence: 3 CAC GTG GAG TGA GGT CTC CTC 5 (template strand) Allele 1: 3 CAC GTG GAG TGA GGT CTC CTC 5 (template strand) Allele 2: 3 CAC GTG GAG TGA GGT CAC CTC 5 (template strand)

10 Age: 23 year old female Ethnicity: European ancestry Patient 2 Healthy: tonsillectomy as child; jogs daily; eats healthy; non-smoker; drinks occasionally; regular menstrual cycles, but started at age 10. Family history Aunt had breast cancer Grandmother died of undiagnosed cancer 23andMe gene of interest: BRCA1 BRCA1 gene: 5589 nucleotides (without introns); codes for 1863 amino acids; Kda Partial Normal sequence 30 bases from start: 3 GTG ACA GAC AGT GAT CCG TAT CCC ATT 5 (template strand) Patient Allele Sequence: Allele 1: 3 GTG ACA GTG ATC CGT ATC CCA TT5 (template strand) Allele 2: 3 GTG ACA GAC AGT GAT CCG TAT CCC ATT 5 (template strand)

11 Patient 3 29 year old female; Has European and and Japanese ancestry Has 1 month old son and 6 year old daughter Family history Had a brother who died at age 8; only remembers him having seizures and interesting brittle hair. Sister has 3 healthy daughters and 1 healthy son. 23andMe gene of interest: ATP7A ATP7A gene: 4500 nucleotides (without introns); codes for 1500 amino acids; Kda Partial Normal sequence (start at position 3138) 3 ACA CCC TGG GAC TTT CGG GCC TTC 5 (template strand) Patient Allele Sequence: Allele 1: 3 ACA CCC TAG GAC TTT CGG GCC TTC 5 (template strand) Allele 2: 3 ACA CCC TGG GAC TTT CGG GCC TTC 5 (template strand)

12 Patient 4 23 year old female of Mediterranean and Jewish Ancestry Had trouble having a child, but now has 1 healthy son. She is currently 2 months pregnant. Family history: Niece died at age of 2 years old Grandparents often spoke of many babies not living long in their family. 23andMe gene of interest: HEXA HEXA gene: 1587 nucleotides (without introns); codes for 529 amino acids; Kda Partial Normal sequence in exon 1: GGG TCC CAT TTT GCA CTT CCC TGC (template strand) Patient Allele Sequence: Allele 1: GGG TCC CAT TTT GCA CTT CCC TGC Allele 2: GGG TCC CAT ATT GCA CTT CCC TGC (template strand) (template strand)

13 Patient 5 Ethnicity: Mother from Italy and Father from Egypt Age: 40 years old Health: Excellent health; exercises daily; low stress; occasional drink; nonsmoker. Family history: Relatively good health on both sides of family; father side there is high blood pressure. Gene of interest from 23andMe: HTT HTT gene: 9426 nucleotides (without introns); codes for 3142 amino acids; KDa Partial Normal sequence in the first exon: 3 CAC (GTC)X6 GTG GAG TGA GGT CTC 5 (template strand; note that this is not the actual sequence of the gene) Patient Allele Sequence: Allele 1 3 CAC (GTC)x36 GTG GAG TGA GGT CTC 5 (template strand) Allele 2: 3 CAC (GTC)X6 GTG GAG TGA GGT CTC 5 (template strand)

14 Patient 6 8 year old boy from Ohio. Has a 1 year old brother and a 3 year old sister. Mother and father are healthy and the family is a very active family (boating, camping, biking, etc.) He has a very unusual and suspicious mole on his cheek. It has been biopsied but tests are not back. 23andMe gene of interest: XPA XPA gene: 819 nucleotides (without introns); codes for 273 amino acids; 31,368 KDa Partial Normal sequence 30 bases from start: GTG ACA GAC CTT GAT CCG TCC (template strand) Patient Allele Sequence: Allele 1: 3 GTG ACA GTG CCT CGT ATC CCA 5 (template strand) Allele 2: 3 GTG ACA GAC CTT GAT CCG TCC 5 (template strand)

15 Patient 7 Female Fetus who is 30 weeks gestational age. Father has hemophilia and is from Cuba Mother is healthy and has had an unremarkable pregnancy and is also from Cuba They send moms sequence off to 23andMe. Gene of interest from 23andMe: F8 F8 gene: 7053 nucleotides (without introns); codes for 2351 amino acids; KDa Partial Normal sequence 3 ACA CCC TGG CCC TTT CGG GCC TTC5 (template strand) Patient Allele Sequence: Allele 1: 3 ACA CCC TGG CGC TTT CGG GCC TTC5 (template strand) Allele 2: 3 ACA CCC TGG CCC TTT CGG GCC TTC5 (template strand)

16 Patient 8 Ethnicity: Born in small village in Germany, as were both his parents. Age: 28 years old Health: low level of exercise; fatty diet; overweight (but not obese); believes he is infertile; no breathing problems. Family history: Several males on both sides of his family have had infertility problems; diabetes on mother side. Gene of interest from 23andMe: CFTR CFTR gene: 9426 nucleotides (without introns); codes for 3142 amino acids; KDa Partial Normal sequence in exon 10: GUG AUG 3 CAC GTG GAG TGA CAC CTC GGC 5 Patient Allele Sequence: Allele 1 3 CAC GTG GAG TGA TAC CTC GGC 5 (template strand) Allele 2: 3 CAC GTG GAG TGA CAC CTC GGC 5 (template strand)

17 pi Table and Genetic Code

c Tuj1(-) apoptotic live 1 DIV 2 DIV 1 DIV 2 DIV Tuj1(+) Tuj1/GFP/DAPI Tuj1 DAPI GFP

c Tuj1(-) apoptotic live 1 DIV 2 DIV 1 DIV 2 DIV Tuj1(+) Tuj1/GFP/DAPI Tuj1 DAPI GFP Supplementary Figure 1 Establishment of the gain- and loss-of-function experiments and cell survival assays. a Relative expression of mature mir-484 30 20 10 0 **** **** NCP mir- 484P NCP mir- 484P b Relative