The Cohen gene so-called may prove to be a marker of ancient Middle East populations. Its absence or presence does not necessarily indicate Judeans versus Northern Kingdom. The point of the Times of India article was that both in the case of the Jews of Cochin (Black, White and Meshuhrarim [=freedslaves]) and the Bene Israel there is sure evidence linking them both to the ancient Middle East.
I have not been involved in collecting DNA from the Bene Menasheh although I believe colleagues in Israel are conducting genetic research on them. However I did collect from the Telugu-speaking community in Guntur Province and the results as the Times of India article indicated were neutral. They were not negative, they were neutral. That is, no particular markers linking them to any of the populations for which markers are known were found.
The research in no way invalidates the Telugu-speaking community’s claims to be viewed as Jews. During my recent research visit among this community I was impressed by the sincerity and devotion of this community who maintain a synagogue in a large, very poor village which has 2 mosques, a thousand Hindu temples, and several dozen churches. Whereas the churches are beneficiaries of help from abroad particularly from Europe and the USA, the synagogue is not. I receive almost daily pleas from the community — not for money but for my help in acquiring rabbinic instruction for their teachers.
In my view these people are as “Jewish” as their cousins in Manipur, yet strangely they are ignored.