2. HGP (1990 – 2003)

Which statements regarding the Human Genome Project (HGP) are correct?

1) In order to make a physical map of the human genome mainly non-polymorphic markers were used

2) ESTs were generated by sequencing cloned cDNA

3) Most of the sequence data for the human genome was generated by shotgun sequencing of BACs

4) Sanger sequencing was not yet invented when the HGP started

5) With the available technology at the start of the HGP, it would have taken over 50 000 years per person to sequence the human genome

Which statements regarding mapping the human genome are correct?

1) Larger DNA fragments can be cloned when using BACs than when using normal plasmids, because BACs have fewer copy numbers per E.coli cell

2) BACs were used as the main cloning system as they allowed to sequence the inserts completely from both sides in just two sequencing reactions

3) Reverse transcriptase is only needed for cDNA libraries but not for DNA libraries

4) The density of SNPs in a genome is always larger than the density of RFLPs

5) Microsatellites are often polymorphic due to their high mutation rates

Which statements regarding Sanger sequencing are correct?

1) ddNTPs are needed for Sanger sequencing to label newly synthesized DNA during the reaction

2) the ratio of ddNTPs to dNTPs needs to be >10x as otherwise too few DNA strands get terminated

3) the ratio of ddNTPs to dNTPs needs to be <<100x as otherwise one cannot read far enough

4) Radioactive Sanger sequencing always requires four different reactions and four different lanes to determine one sequence

5) In one Sanger sequencing reaction one can sequence on average ~2000 bp

6) How many basepairs can be sequenced in one sequencing reaction depends mainly on the resolution of the gel

Which statements regarding sequencing during the Human Genome Project (HGP) are correct?

1) As making the physical map of BAC clones took longer than anticipated, the HGP produced the sequence data first and then assembled the BAC clones using the physical map

2) BAC clones were sequenced in overlapping fragments by insert-specific primers (“primer walking strategy”)

3) BACs were sequenced by randomly shearing the BAC inserts, cloning the resulting fragments into plasmids and sequencing those using primers located in the plasmid

4) BACs were sequenced by cutting BAC inserts with restriction enzymes, cloning the resulting fragments into plasmids and sequencing those using primers located in the plasmid

5) Getting a BAC sequence from draft to finished quality usually requires to manually plan sequencing reactions to fill gaps in the sequence of the BAC insert

A phred quality score of 10 means that…

1) A position was covered 10 times

2) A contig contains less than 10% errors

3) A contig is at least 10kbp long

4) The sequence base at this position is two times more likely to be not called correctly than a sequenced base with a Phred quality score of 20

5) The sequenced base at this position is called corretly with 90% certainty

Which statements regarding Genome Assemblies are correct?

1) Long, repetitive sequences in the genome are a major problem for genome assemblies

2) For a given genome, usually several assembly versions exist

3) Components, Contigs and scaffolds are different levels of an assembly

4) An N50 contig length of 100 000 is better than a N50 contig length of 50 000

5) In 2004 a finished version of the human genome was published that by definition did not contain any gaps