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So it is relatively easy to find out which genes are on the X chromosome. But what about the autosomal chromosomes? The first time a gene was mapped to an autosomal chromosome was in 1968. Roger Donahue, then a research student, looked at his own chromosomes under a microscope and found that one of his chromosomes-1 was slightly longer than in most people. Further research revealed that all the members of his family who had this longer version of chromosome-1, also carried the allele for a particular type of blood group called Duffy-a. All the members of his family who had the normal chromosome-1 did not have this allele. This provides strong evidence that the locus for this gene is linked to this tiny extra bit of chromosome-1. This approach soon led to many other genes being assigned to human autosomal chromosomes.
However, this approach relies on finding visible chromosome mutations - typically deletions, duplications or translocations. A much more efficient way of gene mapping human genes to chromosomes arrived with the advent of human-mouse hybrid cells called somatic cell hybrids. It is possible to fuse a somatic (i.e. diploid, no-germline) human cell with a somatic mouse cell and establish a resulting cell line which reproduces itself by mitosis. Perhaps unsurprisingly though, such a cell line has problems maintaining its full chromosome complement. Over time, it tends to lose chromosomes. You can therefore end up with cell lines which have a lot of mouse chromosomes but only one pair of human chromosomes, e.g. chromosome-4.
This means that any human proteins that this cell line makes must be coded for by genes on human chromosome-4. Somatic cell hybridisation and other more recent approaches have meant that human gene mapping, while still involving a great deal of hard work, is becoming increasingly routine.