Lecture 4: Genomics in Modern Medicine

What is the definition of genomic medicine according to NHGRI?

A structured approach to disease discovery, diagnosis, and management that prominently features next‑generation sequencing and analysis.

Why did genomics make sense for evaluating Case 1, the family with skeletal dysplasia?

Negative SHOX testing, heterogeneous skeletal dysplasias, multiple affected children, consanguinity, and need for surgical planning.

What gene was ultimately implicated in Case 1, the family with skeletal dysplasia?

HAPLN1, with a homozygous 1‑bp deletion.

What is the predicted effect of the HAPLN1 deletion?

Premature truncation and likely degradation of the protein.

What phenotype did the Hapln1 knockout mice show?

Severe chondrodysplasia, shortened snout, shortened limbs, underdeveloped skull base ossification, and malformed ossicles

What is the significance of the Human Genome Project for modern genomics?

It provided the first draft human genome after 13 years and ~$2.7B, enabling modern sequencing approaches

What is next‑generation sequencing (NGS)?

Massively parallel sequencing technologies enabling rapid interrogation of DNA, including whole genomes.

What percentage of the genome encodes proteins?

1-2%

What proportion of human variation is due to single nucleotide variants (SNVs)?

75% of all DNA changes

What is the frequency of single nucleotide variants (SNVs) in the genome?

1 in ever 100-300 nucleotides

What are indels?

Insertions/deletions up to 50–100 nt; occur 1/10 as often as single nucleotide variants (SNVs)

What are copy number variants (CNVs)?

Structural genomic alteration where the number of copies of a specific DNA segment varies between individuals

What is the purpose of library preparation in next‑generation sequencing (NGS)?

Fragment DNA and add adapters, primers, and barcodes for sequencing

What is shotgun sequencing?

Random fragmentation of DNA prior to sequencing

What is enrichment in next-generation sequencing (NGS)?

Selecting specific genomic regions (e.g., exons) using capture probes

What is the role of bioinformatics in next-generation sequencing (NGS)?

Alignment, variant calling, annotation, and interpretation — a major part of the workflow

What is the typical number of variants found in a whole genome?

4 million

What phenotype is associated with PLS3 mutations?

Childhood‑onset osteoporosis, fractures, and hypermobility

Genomic medicine prominently features _______

Next‑generation sequencing (NGS)

Indels occur about _____ as often as SNVs.

1/10

PLS3 is associated with ______ inheritance.

X‑linked dominant

______ can involve genes such as AMELX, AMTN, and ENAM.

Amelogenesis imperfecta

True or False: CNVs are the most common type of variant.

False: SNVs are most common; CNVs affect more nucleotides.

What clinical features in Case 1 suggested a skeletal dysplasia?

Mesomelic dysplasia, flat face, elbow dislocation, severe pectus carinatum, oligodontia, cleft palate

Why was SHOX testing insufficient in Case 1?

Symptoms matched a known syndrome, but SHOX testing was negative, suggesting a different genetic cause

What year was Sanger sequencing published?

1977

What year was the human genome first published?

2001

What is multiplexing in Sanger sequencing?

Running multiple small panels simultaneously to increase throughput

What is the main advantage of next-generation sequencing (NGS) over Sanger?

Massively parallel sequencing enabling whole genomes/exomes

What is the purpose of enrichment in next-generation sequencing (NGS)?

To isolate specific genomic regions (e.g., exons) for sequencing.

True or False: SNVs are the most common type of variant.

True

True or False: CNVs affect fewer nucleotides than SNVs.

False: CNVs affect more nucleotides overall.

What is the relationship between variant size and frequency in the genome?

maller variants (SNVs) are more frequent, while larger variants (CNVs, structural variants) are less frequent but affect more nucleotides.

What is the purpose of variant annotation?

To determine whether a variant is pathogenic, benign, or uncertain.

What is the first step in variant detection after sequencing?

Alignment of reads to the reference genome

What is consensus calling?

Determining the most likely genotype at each position based on read data

What is the purpose of filtering variants by allele frequency?

To remove common variants unlikely to cause rare disease

What is the typical number of variants in an exome before filtering?

300,000

What is the main challenge of NGS variant interpretation?

Distinguishing pathogenic variants from benign background variation

What is the purpose of using a reference genome?

To identify differences between patient DNA and the standard sequence.

What type of CNVs are most reliably detected by NGS?

Exonic‑level deletions/duplications.

What dental phenotype has been reported in PLS3‑related disease?

Opalescent teeth (case‑report level).

What is the advantage of pooling samples before enrichment?

Reduces cost and time while increasing throughput

What is the purpose of the UCSC Genome Browser in probe design?

To visualize exons, introns, and genomic coordinates for capture probe selection

What is the purpose of massively parallel sequencing?

To sequence millions of DNA fragments simultaneously

What is the purpose of sequencing by synthesis (SBS)?

To incorporate fluorescent nucleotides one at a time and detect them

What is the role of lasers in Illumina sequencing?

To excite fluorescently labeled nucleotides for detection

What is the purpose of alignment algorithms like BWA or Bowtie?

To map sequencing reads to the reference genome

What is the purpose of variant calling?

To identify differences between patient DNA and the reference genome

What is the purpose of IGV (Integrative Genomics Viewer)?

To visualize sequencing reads and confirm variants manually.