Human Genome Project by Lim Zhen Huang

Goal

2024-03-29 00:34:56 UTC

It is to determine the sequence of the four chemical groups called bases in all of the strands of DNA contained in the chromosomes of every human cell.

2024-03-29 00:35:31 UTC

2024-03-29 00:46:24 UTC

Definition

2024-03-29 00:50:13 UTC

It is an ambitious research effort aimed at deciphering the chemical makeup of the entire human genetic code

What about designer babies? Or living forever?

d7fccg2c4y — 2024-03-29 00:55:37 UTC

Many say here is where we must hold the line: gene-editing should be a rare tool for eliminating serious disease only. But others, see the line between medicine and enhancement as too blurry to last forever. What if a cure for Alzhiemer’s disease came with the side-effect of enhanced memory? Or suppose we could edit out disease altogether - engineering our hearts never to fail, or our cells never to become cancerous?

Gene VS Genome

2024-03-29 00:56:08 UTC

Sequence: A sequence refers to the specific order of nucleotides (the building blocks of DNA) along a stretch of DNA. In other words, it's the arrangement of adenine (A), thymine (T), cytosine (C), and guanine (G) bases that make up the DNA molecule. Each organism has a unique DNA sequence, and variations in the sequence can give rise to differences in traits and characteristics.
Fragment: In the context of DNA sequencing, a fragment refers to a portion of DNA that has been broken or cleaved into smaller pieces. These fragments are typically generated during the process of preparing DNA for sequencing, and they are then sequenced individually. The sequence data obtained from these fragments are later assembled to reconstruct the entire genome sequence.

2024-03-29 00:59:02 UTC

• Secure against threads - secure against unauthorised access to data

• Flexible - able to submit different queries

• Privacy-preserving - never disclose individual-level information of people

• User-defined and auditable data-control - self-executing protocols that can change the blockchain global state

✅ end-to-end protection of data

✅ Multiple layers of privacy protection

Disadvantages of human genome project (HGP)

2024-03-29 01:00:50 UTC

Technologies limitation

Limit the development of advance sequencing technologies
Incomplete genome sequencing

Cost limitations

Expensive
Improper allocation of resources

Privacy concern

Raises significant privacy issues regarding the confidentiality and control of genetic information.

Genetic discrimination

Progress

d7fccg2c4y — 2024-03-29 01:02:52 UTC

Current IVF screening has itself reduced the rate of babies born with non-life-threatening conditions such as Down Syndrome and dwarfism, and skewed gender demographics in countries such as India and China. Many fear that disability, not just disease, will increasingly become the target of genetic erasure as the technology advances – embryos likely to have bipolar disorder or deafness may no longer be considered viable either. And it doesn’t take too much imagination to see how a “designer baby” scenario could rapidly open a new and likely unbridgeable class divide between those who can afford to be enhanced and those you cannot.

Eugenics concerns

2024-03-29 01:03:15 UTC

Curing genetic disease sounds almost entirely ethical. The only way it wouldn’t be ethical is because of the current state of genetic engineering research. We don’t know much about it, and it could go easily wrong. But, if the person undergoing the genetic modification was able to consciously agree to the risks, it wouldn’t be unethical. Genetic enhancement of “designer babies” could lead to social pressure if this is abused by the society. This is due to it creating a certain standard of “superior” traits potentially exacerbating existing inequalities and leading to discrimination against those who are not genetically enhanced.

4. Genome assembly

2024-03-29 01:10:03 UTC

The process of putting nucleotide sequence into the correct order
It is needed because DNA sequencing technology cannot read whole genomes in one go
assemble the fragments into longer contiguous sequences, called contigs
This process involves aligning overlapping sequences and filling in gaps to reconstruct the entire genome sequence.

There are two different types of genome assembly:

de novo assembly: genome assembly of a novel genome from scratch without the aid of reference genomic data
mapping to a reference genome (also known as reference-based alignment): A reference genome or a reference assembly is a digital nucleic acid sequence database, acting as a representative example of a species’ set of genes. Once the reference genome is available, with its aid, the genome assembly becomes much easier, quicker, and even more accurate. Therefore, unless necessary, researchers choose the method of reference based alignment. Reference-based alignment has become the current standard in diagnostics.

Advatange of Human Genome Project (HGP)

zhixin1117 — 2024-03-29 01:10:57 UTC

Revolutionised the understanding and treatment of genetics disease
- improved diagnosis, novel therapeutic approaches
- development of more specific diagnostic tests for various genetic conditions
  (Eg: myotonic dystrophy, Alzheimer's disease, and inherited colon cancer)
Improve yield:
- created stronger, more disease-resistant plants and animals
- reducing agricultural costs and providing healthier, pesticide-free foods

Storytime!!

d7fccg2c4y — 2024-03-29 01:11:45 UTC

When the twin girls were born, one October night in 2018, they carried a secret: a hidden tweak in their DNA even the hospital in China didn’t know about. They were the world’s first genetically engineered humans.

The next month, news of their existence broke just as the scientist behind the engineering, Dr He Jiankui, was addressing peers at a global summit. Facing down an uncharacteristically rowdy hall of scientists, he explained: with fertility treatments illegal for prospective parents with HIV in China, he had instead edited the girls as embryos to be resistant to the AIDS virus carried by their father. He said genetic testing showed that “Lulu” and “Nana” were “as healthy as any babies”. Their real identity is now a state secret in China and it is not known how they are doing.

But Dr He has been jailed for three years and his research internationally condemned as rogue “Frankenstein” science. He had faked tests, kept doctors in the dark, and bypassed ethics boards in his quest to be the first to “cross the germline” and engineer humans. Some even suspected he had targeted the specific gene in question not only because it was linked to HIV infection but because it had been shown to boost brain power, when removed in mice. What had been feared by many in the scientific community, especially since the creation of the breakthrough gene-editing tool CRISPR, had come to pass.

Inequality and Social Justice

2024-03-29 01:14:04 UTC

The ability to afford genetic enhancements could exacerbate existing socioeconomic inequalities, widening the gap between those who can afford enhancements and those who cannot, further entrenching social injustices.

2024-03-29 01:16:34 UTC

Isolation of DNA
- By blood samples, tissue biopsies, or cell cultures
- DNA extracted to break open the cells & separate DNA from other cellular components
Fragmentation of DNA
- By using enzymes to cut DNA at specific sequences, or by physical methods (sonication & nebulization)
- Necessary as current DNA sequencing technologies only sequences short stretches of DNA at the time
DNA sequencing
- Sanger sequencing- dideoxy chain termination sequencing (most widely used method)
- Primer annealing - To form fragmented DNA, primer provide starting point for DNA polymerase to synthesise new DNA strands
- DNA synthesise with modified nucleotides- dideooxynucleotides (ddNTPs), incorporates into a growing DNA strand, terminates further elongation
- Fragment separation - Conducted in four tubes with different ddNTP, terminated fragments of different lengths are produced, each terminating with a specific ddNTP
- Gel electrophoresis - Terminated DNA sequences separate by size, gel exposed to source of fluorescence, allows visualisation of DNA fragments, where shortest fragments move to furthest
- Reading the sequences of bases in DNA fragments
  - Determine by analyse pattern of bands on gel
  - Identify position of each terminated fragment & correlate with ddNTP used in synthesise reaction

5. Annotation and Analysis

2024-03-29 01:17:15 UTC

DNA annotation or genome annotation is the process of describing the structure and function of the components of a genome, by analyzing and interpreting them in order to extract their biological significance and understand the biological processes in which they participate.

The assembled genome sequence is then annotated, which involves identifying genes, regulatory elements, and other functional elements within the genome.

Bioinformatics tools are used to analyze the genome sequence for various purposes, such as identifying genetic variations, studying gene expression patterns, and understanding the genetic basis of diseases.

zhixin1117 — 2024-03-29 01:21:04 UTC

International collaboration and data sharing
- facilitated the pooling of resources, expertise, and data
- the open policy of sharing data within the HGP and other international collaborations has promoted transparency, innovation, and the rapid dissemination of knowledge.

6. Data Sharing and Integration

2024-03-29 01:24:31 UTC

The genome sequence data generated by the HGP and subsequent projects are made publicly available in databases such as GenBank and the Genome Browser, allowing researchers around the world to access and analyze the data for their own research.

Background

2024-03-29 01:24:55 UTC

The HGP operated from 1990 to 2003, provides researchers with basic information about the sequence of 3 billion chemical base pairs. The HGP was further intended to improve the technologies needed to interpret and analyse genomic sequence, to identify all the genes encoded in human DNA to address the ethical, legal, an social implications that might arise from defining the entire human genomic sequence.

2024-03-29 01:29:17 UTC

Should we agree to give government and insurance companies to access the genetic informations of an individuals?
Shouldn’t we worry that such information could be used to restrict our civil liberties?
Do we want insurance companies to be able to deny medical insurance to exactly those people who may need it the most?