Bio 305- Chapter 11

Variations in the number of copies of large blocks of DNA (greater than 10 bp and up to 1 Mbp) are referred to as

CNVs

Patients with what disease are often compound heterozygotes for the disease allele?

Cystic fibrosis

What type of genetic variation involves short insertions or deletions of genetic material?

DIPs

DNA _______ serve as signposts in the genome

DNA marker

A silicon chip containing small fragments of single-stranded DNA is called a ________ ________

DNA microarray

What technology takes advantage of allele-specific oligonucleotides?

DNA microarray

Genes who mutant alleles cause a disease phenotype are called ________ genes

Disease genes

T of F: A single fluorescently labeled DNA molecule generates enough light to allow its detection on a microarray

False

A genetic disease that can be caused by a variety of different mutations in the same gene displays allelic _______

Heterogeneity

In a rare dominant condition, it is highly likely that the patient will be _________ for the causative allele

Heterozygous

The ability to rapidly sequence large amount of DNA is called _______-_______ sequencing.

High-throughput

What is the goal of positional cloning?

Identify genetic mutations that are associated with hereditary diseases.

Polymerase chain reaction was developed by

Kary Mullis

Primers are chosen for PCR based on

Knowing the DNA sequence on both sides of the target region

A ________ score is used to determine whether available data are sufficient to conclude with confidence whether a disease gene and a DNA marker are genetically linked

LOD

How is the relative frequency of DIPs related to their length (if at all)?

Longer DIPs are much less frequent than shorter DIPs

the sequencing of the entire genomes of all members of a nuclear family was first done in looking for the mutation that causes

Miller syndrome

The ability of complementary single strands of DNA or RNA to come together to form double-stranded molecules is called ______ acid ______.

Nucleic acid hybridization

Single ________ ______________ are particular base positions in the genome where alternative nucleotides distinguish some people from others

Nucleotide polymorphism

One limitation to positional cloning is that you must be able to determine the ________ of the SNP and disease alleles for the people in the pedigree

Phase

What genetic variation involves sequences of one to a few bases that are repeated in tandem less that 10 to more than 100 times within the genome?

SSRs

Select probe/target hybrid that will stay hybridized at a higher temperature

Stand held together, no bumps/bends. Two straight strands connected.

One of the technological innovations that has made high-throughput sequencing possible is the ability to control base addition ________ so that each base can be identified before the next one is added.

Temporally

In PCR, the template DNA is

The DNA to be amplified

A Lod score is used in human genetics rather than a x2 statistic because

The Lod score better handles the small number of data points while allowing the data obtained from many different pedigrees to be combined

Whole-exome sequencing, scientists first enrich for genomic DNA fragments that correspond to exons of all genes by hybridization to

cDNA sequences

If a genetic condition is recessive and the parents are not even distantly related, the patient might be a _____ heterozygote

compound

Patients that have one copy of a gene with one mutation, and the other copy of the same gene with a different mutation are called __________ heterozygotes

compound

The process of human genetics requires that _______ remain up to date and that their information is available to all investigators

databases

When using PCR to amplify DNA, short oligoneucleotides called primers

define the ends of the target region of DNA

In PCR, primers bind to

denatured (single-stranded) template DNA

DNA polymorphisms are

differences in any DNA sequences between individuals

Because whole-genome sequencing is still expensive, some researchers instead do whole-_______ sequencing.

exome

In positional cloning, at least one parent must be a double ________ for the cross to be informative.

heterozygote

The association of a molecular marker that is transmitted along with a genetic disease in a family pedigree indicates that the molecular marker _______.

is likely to be close to the gene that causes the disease

Simple sequence repeats, which are one to a few bases repeated in tandem within the genome, are also called _______

microsatellites

Another name for the configuration of alleles is their

phase

Because each individual's genome contains millions of _______, scientists may have trouble identifying which change is responsible for for a disease

polymorphisms

the first goal of ______ cloning is to discover a DNA marker that shows linkage to the disease locus

positional

In the bioinformatics analysis that identified mutations in the XIAP gene as being responsible for Nic Volker's symptoms, a filter for________ conserved sequences looked to see if Nic's genome contained changes in sequences that are the same in many diverse species.

tightly

The majority of cystic fibrosis patients have what mutation?

ΔF508

Choose all that apply to a final PCR product

-Extends from one primer's 5' end to the position of the others 5' end -double-stranded

Uses for DNA fingerprinting

-Forensics -Paternity suits -Identification of human remains

How might a non-actionable outcome of whole genome sequencing to identify a disease gene still provide useful information?

-May provide information that helps identify a future treatment for the disease -May help patients to guide their reproductive decisions

Types of variants that are likely to be nonanonymous polymorphisms

-Missense mutation -Nonsense mutation -Frameshift mutation

Select problems that may impede a geneticist's ability to identify the mutation responsible for a disease

-The amount of variation among human genomes is huge -No genome sequence is 100% complete

A Lod score is calculated from the ____ of the probability of obtaining a particular set of results in a _______ is two loci are linked to the probability of observing the same results if the loci are unlinked

-ratio -pedigree

In a rare dominant condition it is likely that

-the patient will be heterozygous for the causative allele -related patients will have the same rare mutant allele -unrelated patients might have a different mutation in the same gene

Steps in one cycle of a PCR reaction

1) Denaturation of target DNA into single strands 2) Hybridization of primers 3) Polymerization by DNA polymerase

Why does PCR require a special DNA polymerase from a bacterium that grows in hot springs?

After each round of replication, the PCR reaction is heated to melt apart the DNA strands and the polymerase must remain active at this temperature

How many SSR loci per person are examined and cataloged in the CODIS database?

13

The National Center for Biotechnology Information has cataloged more than 50 million SNPs that are found in human genomes. How many of these are considered to be common in human genomes?

15 million

On average, a disease causing gene should lie within _______ of one polymorphic locus on a DNA microarray

3 Mb

The identification of a disease gene that provides information on how a condition might be treated is called an ________ outcome.

Actionable

Polymorphisms that change the size of a locus can be genotyped after PCR without sequencing using

Gel electrophoresis

Genetic variants that affect phenotypes through changes in protein function are called ________ DNA polymorphisms

Nonanonymous

Examining multiple polymorphic ______ loci is a powerful resource for identifying a person fro his or her DNA

SSR

A method for obtaining fetal cells in a sample of the fluid surrounding the fetus is called

amniocentesis

Sequence differences between genomes that affect neither the nature nor the amount of any protein in the body called ____ DNA polymorphisms

anonymous

The _______ is the collection of all exons of all genes

exome

Prenatal __________ __________ involves genotyping fetal cells by methods such as PCR.

genetic diagnosis

Two genes are _________ if they are positioned close together on the same chromosome

linked

Molecular markers can be used to identify the location of a disease-causing gene because they

may be located close to a disease-causing gene

The strategy in which the location of a gene associated with a hereditary disease is identified by finding polymorphic loci to which the mutation is genetically linked is called

positional cloning

Embryos produced by in vitro fertilization can undergo genetic testing prior to being placed in the mother's womb by

preimplantation embyro diagnosis

Short oligonuleotides that flank the region of DNA to be amplified by PCR are called ________.

primers

In trying to determine the mutation responsible for Millers syndrome, scientists studied a family in which two children of unaffected parents were affected. To narrow down the sequence data, scientists focused on regions where the affected son and daughter

share the same allele from the mother and also the same allele from the father

In PCR, DNA polymerase adds nucleotides onto

the 3' ends of primers

An actionable outcome came from the bioinformatics analysis behind variations in what gene?

-CFTR -XIAP

PCR involves denaturation of target _____ into single strands, hybridization of ______, and polymerization by DNA ______.

- region - oligonucleotides - polymerase

Select reasons that very few differences in DNA sequences between two people alter the amino acid sequences of proteins

-A very small percentage of the human genome consists of codons within genes - Natural selection might lead to the disappearance of deleterious mutations - Many mutations within codons are silent

The National Center for _________ Information has a catalog of more that 50 million single nucleotide _________ found in the human genome

-Biotechnology -polymorphisms

Conditions that display locus heterogeneity

-Deafness -High blood pressure

Select filters that were used in the bioinformatics analysis that identified mutations in the XIAP gene as being responsible for Nic Volker's symptoms

-Filters for novel variants -Filters for recessive inheritance -Filters to exclude silent mutations

What types of polymorphisms can be genotyped by performing PCR and then separating the PCR products by gel electrophoresis (without sequencing)?

-SSRs -DIPs

Steps shown in this figure of high-throughput, single molecule DNA sequencing

-Single stranded genomic DNA is attached to a flowcell -DNA polymerase synthesizes new DNA containing nucleotides with colored, base-specific fluorescent, and with blocks on their 3' end -A high-resolution camera photographs the fluorescence, and the tag and blocking groups are removed from the most recently added nucleotides -New DNA polymerases and labeled, blocked nucleotides are added to the flow cell, and the reaction is repeated about 100 times

Reasons a mutation may remain unidentified even when a whole-genome sequence is available

-The mutation may affect transcription of the disease gene -The mutation may affect splicing of the disease gene's transcript

What new innovations are used in high-throughput sequencing?

-The sensitivity of detection is so high that a single molecule of DNA can be monitored without the need for cloning or PCR amplification -Individual DNA molecules are synthesized by DNA polymerase anchored in one piece - Base addition is controlled temporaily so that each base can be identified before the next one is added

Molecules that can undergo nucleic hybridization

-Two complementary single-stranded DNAs -Two complementary single-stranded RNAs -A single-stranded DNA and a complementary single-stranded RNA

The technique of sequencing PCR products amplified from genomic DNA can be used to genotype

-expansions/contractions of the number of repeats in SSRs -SNPs -small DIPs

Positional cloning can be thought of as a high-throughput way to perform thousands of two-point crosses to test for ________ between an individual DNA marker and the ______ locus.

-linkage -disease

Genetic variants in order from most frequent to least frequent in human genome

1) SNP (Single neucleotide polymorphism) 2) DIP (Insertion/deletion) 3) SSR (Simple sequence repeat) 4) CNV (Copy number variant)

Steps in order in determining a Lod score

1) Tabulate which progeny are parental and which are recombinant 2) Calculate the Lod score numerator and denominator 3) Calculate the likelihood ratio 4) Calculate the Lod score 5) Interpret the Lod score

A genotype for 13 unlinked, polymorphic SSR loci can serve as a DNA _______

Fingerprint