Human Genome Project

Front 1

Copy Number Variants (CNVs)

Back 1

-sequence that is at least one kilobase in length and polymorphic. This definition may vary slightly depending on the source.

-CNVs are roughly defined as being 1-kb or less
in length and polymorphic. It is estimated that we have 1,000 CNVs in our genomes. Different human genomes may vary from 4 – 24 MB in length. CNVs are still under study since human genome sequences tend not to be as accurate in assessing their abundance. It is important to appreciate that genomic abnormalities are found in individuals with a wide
array of common diseases and their role in disease pathogenesis is becoming increasingly appreciated

Front 2

de novo mutations

Back 2

a sequence change that is present for the first time in one family member as a result of a mutation in a germ cell of one of the parents or in the fertilized egg.

Front 3

DNA Transposon Fossil

Back 3

Specific type of interspersed repeat element that may or may not encode the proteins necessary for their own replication.

Front 4

Exome

Back 4

The complete exon content of an organism or individual.

Front 5

Hierarchical Shotgun Sequencing Approach

Back 5

Approach where large, overlapping DNA fragments
of known location in the human genome were subject to shotgun sequencing. The sequences of these large fragments were then used to determine the sequence of the human genome.

Front 6

Interspersed Repeats

Back 6

specific class of repeat sequences in the human genome that range from one hundred to three thousand base pairs. They consist of LINE, SINE, and retrovirus-like elements as well as DNA transposon fossils.

Front 7

LINEs

Back 7

Long interspersed nuclear elements are a specific type of interspersed repeat element that encode the proteins necessary for their own replication.

Front 8

Retrovirus-Like Elements

Back 8

Specific type of interspersed repeat element that may or may not encode the proteins necessary for their own replication.

Front 9

Segmental Duplications

Back 9

Sequences >1-kb in length that share 90-98% identity. A segmental duplication can contain interspersed repeat sequences.

Front 10

Shotgun Sequencing

Back 10

approach where the DNA sequence of interest is shredded randomly into numerous small fragments and then individual fragments are sequenced. The sequences of these individual fragments are used to determine the sequence of the original DNA sample.

Front 11

SINEs

Back 11

Short interspersed nuclear elements are a specific type of interspersed repeat element that does not encode the proteins necessary for their own replication.

Front 12

Whole Genome-shotgun sequencing

Back 12

approach where a genome of interest is shredded
randomly into numerous small fragments and the sequences of these small fragments are used to
determine the sequence of the whole genome.

Front 13

Human Genome Project

Back 13

The publicly funded effort to sequence the human genome used a hierarchical shotgun approach where large insert clones containing a few hundred kilobases of human genome sequences were isolated and sequenced. This addressed issues arising from the abundance of repeat sequences in the human genome, which make it challenging to assemble our
genome from scratch using a whole genome shotgun approach. The information from the high quality human genome sequence now makes whole genome shotgun sequencing of a person’s genome the preferred approach. Sequencing costs have plummeted in recent years due to new technologies that allow for parallelized, miniaturized, and cost-effective acquisition of raw sequence. It is important to remember that not all human genome sequences acquired to date are of the same quality. ‘Medical genetics quality’ human genome sequences are more costly than draft genome sequences. Furthermore, most cost estimates do not include the bioinformatics analyses to assemble and interpret the sequence information.

Front 14

Exome Sequencing

Back 14

The human genome only contains about 21,000 protein-coding genes. Introns and exons comprise about 30% and coding exons comprise 1.5% of the human genome. It has been estimated that there are at least 180,000 exons in the human genome, which will likely increase as a greater number of RNA transcripts are sequenced. The UCSC Genome Browser (http://genome.ucsc.edu/) is an outstanding resource for obtaining human genome sequence information. Moreover, it is now common and cost-effective to sequence regions of the human genome containing exons, which is called ‘exome sequencing’. This is done by enriching for exon containing genomic sequences in a sample, typically by hybridization, followed by the application of next generation sequencing technologies. It is likely that exons will be missing in any given analysis; however, the vast bulk of the sequences should be represented.

Front 15

Variation among human genomes

Back 15

It is now commonplace to see analyses of human genome sequences in the scientific literature. Studies in the past three to four years focused on comparing the genomes of individuals from different parts of
the world. One of the most striking take home messages is that the levels of genetic variation in different human populations are not the same. In one study, the average rate of nucleotide differences between two native Africans was greater than that observed between a European and Asian individual.

Front 16

Mutation Frequency

Back 16

Please recall that on average every person has:
(i) about 10,000 non-synonymous SNPs that change the amino acid sequence of a protein

(ii) damaging single nucleotide variant (SNV) in 300-400 protein-coding genes

(iii) about 2 bona fide disease-causing mutations

-The above estimates will likely grow as our knowledge of the functional elements in the
human genome increase.

Front 17

De novo Mutations

Back 17

Every person has about 70 de novo mutations in their genome. Severe autosomal dominant disorders that lead to early death prior to adulthood are most commonly caused by de novo mutations. Also, note that variation in de novo mutation rates among families is primarily due to the paternal contribution. It has been observed number of de novo mutations in the offspring increases with paternal age.

Front 18

Prenatal Genome Sequencing

Back 18

Although not ready for clinical implementation, non-invasive fetal genome sequencing (NIFGS) will likely be a reality in the future. This technology takes advantage of the fact that 13% of cell free DNA in plasma of pregnant female is fetal in origin. Like the plasma DNA obtained from maternal cells, the fetal DNA is short and tends to be in the range of about 150-bp in length. This corresponds closely to the length of DNA packed in a nucleosome. Total plasma DNA is sequenced and complex computational analyses are required in order to discriminate between the
sequences derived from the mother and the fetus. One of the current applications is the detection of trisomy 18 (Edwards syndrome), trisomy 13 (Patau syndrome), and trisomy 21 (Down syndrome). The advantage to other traditional prenatal testing technologies (amniocentesis and chorionic villus sampling) is that it is non-invasive and this greatly
reduces the risk of miscarriage due to testing. Whole genome sequencing of fetal genomes is on the horizon; however, there are technical hurdles to be overcome. This technology is accompanied by numerous very serious ethical and social challenges. It is beyond the scope of this lecture to discuss these challenges. Please note that a certified genetic counselor by the name of Charite Ricker will participate in the ICM program.

Front 19

Structural Variation in the Human Genome

Back 19

Interspersed repeats comprise ~45% of the human genome. Segmental duplications are a class of genomic elements that are large and share high percentage identity with another genomic region.
They can encompass entire genes and can contain interspersed repeat sequences. Please be able to recall that segmental duplications >1-kb in length with >90% identity comprise about 4% of the human genome.

Front 20

Annotating the Human Genome

Back 20

The human genome project not only provided a draft version of the human genome. It also spurred technology development that enabled next generation sequencing technologies to arise. These technologies have been applied for a variety of purposes outside of human genome sequencing. For example, they
have been valuable in annotating functional motifs in the human genome, such as enhancer elements, and mapping chromatin structure in human cells. The National Institutes of Health (NIH) launched a large consortium named ENCODE (Encyclopedia Of
DNA Elements), in September 2003, to identify all functional elements in the human genome sequence. This information is valuable for many medical genetics applications, such as defining the genetic basis for disease and searching for new therapies for a variety of diseases.